# EDGAR Filing Document

**Accession Number:** 0001411690
**File Stem:** 0001140361-23-010819
**Filing Date:** 2023-3
**Character Count:** 227551
**Document Hash:** c2d0e4c243b16412a02c871081e2bb3e
**Contains OCR:** False
**Source Format:** 

## Filing Content

## Filing Summary
**0001140361-23-010819.hdr.sgml**: 20230309

**ACCESSION NUMBER**: 0001140361-23-010819

**CONFORMED SUBMISSION TYPE**: POSASR

**PUBLIC DOCUMENT COUNT**: 8

**FILED AS OF DATE**: 20230309

**DATE AS OF CHANGE**: 20230309

**EFFECTIVENESS DATE**: 20230309

**FILER**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** Bionano Genomics, Inc.
- **CENTRAL INDEX KEY:** 0001411690
- **STANDARD INDUSTRIAL CLASSIFICATION:** LABORATORY ANALYTICAL INSTRUMENTS [3826]
- **IRS NUMBER:** 261756290
- **STATE OF INCORPORATION:** DE
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** POSASR
- **SEC ACT:** 1933 Act
- **SEC FILE NUMBER:** 333-252216
- **FILM NUMBER:** 23718288

**BUSINESS ADDRESS:**
- **STREET 1:** 9540 TOWNE CENTRE DRIVE
- **STREET 2:** SUITE 100
- **CITY:** SAN DIEGO
- **STATE:** CA
- **ZIP:** 92121
- **BUSINESS PHONE:** (858) 888-7600

**MAIL ADDRESS:**
- **STREET 1:** 9540 TOWNE CENTRE DRIVE
- **STREET 2:** SUITE 100
- **CITY:** SAN DIEGO
- **STATE:** CA
- **ZIP:** 92121

**FORMER COMPANY:**
- **FORMER CONFORMED NAME:** Bionano Genomics, Inc
- **DATE OF NAME CHANGE:** 20190308

**FORMER COMPANY:**
- **FORMER CONFORMED NAME:** BioNano Genomics, Inc
- **DATE OF NAME CHANGE:** 20120703

**FORMER COMPANY:**
- **FORMER CONFORMED NAME:** BioNanomatrix Inc
- **DATE OF NAME CHANGE:** 20070906

#### **TABLE OF CONTENTS**

#### As filed with the Securities and Exchange Commission on March 9, 2023

#### Registration No. 333-252216

### UNITED STATES <br>

### SECURITIES AND EXCHANGE COMMISSION<br>

### Washington, D.C. 20549

#### POST-EFFECTIVE AMENDMENT NO. 1<br>

#### to<br>

#### FORM S-3<br>

#### REGISTRATION STATEMENT<br>

#### UNDER <br>

#### THE SECURITIES ACT OF 1933 <br>

## Bionano Genomics, Inc.<br>

## (Exact name of registrant as specified in its charter)

---

| | | |
|:---|:---|:---|
| **Delaware** | **3826** | **26-1756290** |
| **(State or Other Jurisdiction of** <br>**Incorporation or Organization)**  | **(Primary Standard Industrial** <br>**Classification Code Number)**  | **(I.R.S. Employer** <br>**Identification Number)** |

---

#### Bionano Genomics, Inc.<br>

#### 9540 Towne Centre Drive, Suite 100<br>

#### San Diego, California 92121<br>
(858) 888-7600<br>

#### (Address, including zip code, and telephone number, including area code of registrant's principal executive offices)
R. Erik Holmlin, Ph.D.<br>

#### President and Chief Executive Officer<br>

#### Bionano Genomics, Inc.<br>

#### 9540 Towne Centre Drive, Suite 100<br>

#### San Diego, California 92121<br>
(858) 888-7600<br>

#### (Name, address, including zip code, and telephone number, including area code, of agent for service)

#### Copies to:

---

| | |
|:---|:---|
| R. Erik Holmlin, Ph.D. <br>**President and Chief Executive Officer** <br>**Bionano Genomics, Inc.** <br>**9540 Towne Centre Drive, Suite 100** <br>**San Diego, California 92121** <br>(858) 888-7600 | **Thomas A. Coll, Esq.** <br>**Phillip S. McGill, Esq.** <br>**Cooley LLP** <br>**10265 Science Center Drive** <br>**San Diego, California 92121** <br>(858) 550-6000 |

---

#### From time to time after the effective date of this Registration Statement<br>

#### (Approximate date of commencement of proposed sale to the public)
If the only securities being registered on this Form are being offered pursuant to dividend or interest reinvestment plans, please check the following box. ☐

If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered only in connection with dividend or interest reinvestment plans, check the following box. ☒

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ☐

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ☐

If this Form is a registration statement pursuant to General Instruction I.D. or a post-effective amendment thereto that shall become effective upon filing with the Commission pursuant to Rule 462(e) under the Securities Act, check the following box. ☒

If this Form is a post-effective amendment to a registration statement filed pursuant to General Instruction I.D. filed to register additional securities or additional classes of securities pursuant to Rule 413(b) under the Securities Act, check the following box. ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of "large accelerated filer," "accelerated filer," "smaller reporting company" and "emerging growth company" in Rule 12b-2 of the Exchange Act.

Large accelerated filer ☐ Accelerated filer ☐ <br> Non-accelerated filer ☒ Smaller reporting company ☒ <br> Emerging growth company ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act. ☐

------

#### **TABLE OF CONTENTS**

#### EXPLANATORY NOTE
This Post-Effective Amendment No. 1 to the Registration Statement on Form S-3 (File No. 333-252216) is being filed by Bionano Genomics, Inc., or the Registrant, because the Registrant expects that it will no longer qualify as a well-known seasoned issuer (as such term is defined in Rule 405 under the Securities Act of 1933, as amended) upon the filing of its Annual Report on Form 10-K for the year ended December 31, 2022. Accordingly, this Post-Effective Amendment No. 1 includes disclosure required for registrants other than a well-known seasoned issuer and makes certain other amendments.

This Post-Effective Amendment No. 1 contains:

&nbsp;&nbsp;&nbsp;&nbsp;• a base prospectus which covers the offering, issuance and sale by the Registrant of the securities identified therein from time to time in one or more offerings with a total value of up to $400,000,000; and

&nbsp;&nbsp;&nbsp;&nbsp;• a sales agreement prospectus supplement that covers the offering, issuance and sale by the Registrant of up to $200,000,000, in aggregate offering price of the Registrant's common stock that may be issued and sold from time to time under a sales agreement with Cowen and Company, LLC.

The base prospectus immediately follows this explanatory note. The specific terms of any securities to be offered pursuant to the base prospectus will be specified in a prospectus supplement to the base prospectus. The specific terms of the securities to be issued and sold under the sales agreement are specified in the sales agreement prospectus that immediately follows the base prospectus. The common stock that may be offered, issued and sold under the sales agreement prospectus is included in the $400,000,000 of securities that may be offered, issued and sold by the Registrant under the base prospectus. Upon termination of the sales agreement, any portion of the $200,000,000 included in the sales agreement prospectus that is not sold pursuant to the sales agreement will be available for sale in other offerings pursuant to the base prospectus.

------

#### **TABLE OF CONTENTS**

#### PROSPECTUS
![](logo_bionanox1.jpg)<br>

$400,000,000

#### Common Stock<br>

#### Preferred Stock<br>

#### Debt Securities<br>

#### Warrants
From time to time, we may offer and sell up to an aggregate amount of $400,000,000 of any combination of the securities described in this prospectus in one or more offerings. We may also offer securities as may be issuable upon conversion, redemption, repurchase, exchange or exercise of any securities registered hereunder, including any applicable antidilution provisions.

This prospectus provides a general description of the securities we may offer. Each time we offer securities, we will provide specific terms of the securities offered in one or more supplements to this prospectus. We may also authorize one or more free writing prospectuses to be provided to you in connection with these offerings. The prospectus supplement and any related free writing prospectus may also add, update or change information contained in this prospectus. You should carefully read this prospectus, the applicable prospectus supplement and any related free writing prospectus, as well as any documents incorporated by reference, before you invest in any of the securities being offered.

#### This prospectus may not be used to consummate a sale of any securities unless accompanied by a prospectus supplement.
Our common stock is listed on the Nasdaq Capital Market under the trading symbol "BNGO." On March 8, 2023, the last reported sale price of our common stock was $1.31 per share. The applicable prospectus supplement will contain information, where applicable, as to any other listing on the Nasdaq Capital Market or any securities market or other exchange of the securities, if any, covered by the applicable prospectus supplement.

We may sell these securities directly to investors, through agents designated from time to time or to or through underwriters or dealers, on a continuous or delayed basis. For additional information on the methods of sale, you should refer to the section entitled "Plan of Distribution" in this prospectus. If any agents or underwriters are involved in the sale of any securities with respect to which this prospectus is being delivered, the names of such agents or underwriters and any applicable fees, commissions, discounts or options to purchase additional securities will be set forth in a prospectus supplement. The price to the public of such securities and the net proceeds we expect to receive from such sale will also be set forth in a prospectus supplement.

***Investing in our securities involves a high degree of risk. You should review carefully the risks and uncertainties described under the heading "Risk Factors" on page [6](#tRF) of this prospectus as well as those contained in the applicable prospectus supplement and any related free writing prospectus, and under similar headings in the other documents that are incorporated by reference into this prospectus.***

**Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus supplement is truthful or complete. Any representation to the contrary is a criminal offense.**

#### The date of this prospectus is March 9, 2023.

------

#### **TABLE OF CONTENTS**

---

| | |
|:---|:---|
|  | **Page**  |
| [ABOUT THIS PROSPECTUS](#tATP) | [ii](#tATP) |
| [PROSPECTUS SUMMARY](#tPS) | &nbsp;&nbsp;[1](#tPS) |
| [RISK FACTORS](#tRF) | &nbsp;&nbsp;[6](#tRF) |
| [SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS](#tFLS) | &nbsp;&nbsp;[7](#tFLS) |
| [USE OF PROCEEDS](#tUOP) | &nbsp;&nbsp;[9](#tUOP) |
| [DESCRIPTION OF CAPITAL STOCK](#tDCS) | [10](#tDCS) |
| [DESCRIPTION OF DEBT SECURITIES](#tDDS) | [13](#tDDS) |
| [DESCRIPTION OF WARRANTS](#tDW) | [19](#tDW) |
| &nbsp;&nbsp;[LEGAL OWNERSHIP OF SECURITIES](#tLOS) | [21](#tLOS) |
| [PLAN OF DISTRIBUTION](#tPD) | [24](#tPD) |
| [LEGAL MATTERS](#tLM) | [26](#tLM) |
| [EXPERTS](#tEXPERTS) | [26](#tEXPERTS) |
| [WHERE YOU CAN FIND MORE INFORMATION](#tWYC) | [26](#tWYC) |
| [INCORPORATION OF CERTAIN INFORMATION BY REFERENCE](#tICI) | [27](#tICI) |

---

i<br>

------

#### ABOUT THIS PROSPECTUS
This prospectus is a part of a registration statement on Form S-3 that we filed with the Securities and Exchange Commission, or SEC, utilizing a "shelf" registration process. Under this shelf registration process, we may offer and sell from time to time in one or more offerings up to a total dollar amount of $400,000,000 of any combination of the securities described in this prospectus.

This prospectus provides you with a general description of the securities we may offer. Each time we offer securities under this prospectus, we will provide a prospectus supplement that will contain specific information about the terms of such securities and offering. We may also authorize one or more free writing prospectuses to be provided to you that may contain material information relating to these offerings. The prospectus supplement and any related free writing prospectus that we may authorize to be provided to you may also add, update or change information contained in this prospectus or in any documents that we have incorporated by reference into this prospectus. If there is any inconsistency between the information in this prospectus and the applicable prospectus supplement or free writing prospectus, you should rely on the prospectus supplement or free writing prospectus, as applicable. You should read this prospectus, any applicable prospectus supplement and any related free writing prospectus, together with the information incorporated herein by reference as described under the heading "Incorporation of Certain Information by Reference," before investing in any of the securities offered.

#### THIS PROSPECTUS MAY NOT BE USED TO CONSUMMATE A SALE OF SECURITIES UNLESS IT IS ACCOMPANIED BY A PROSPECTUS SUPPLEMENT.
Neither we, nor any agent, underwriter or dealer has authorized any person to give any information or to make any representation other than those contained or incorporated by reference into this prospectus, any applicable prospectus supplement or any related free writing prospectus prepared by or on behalf of us or to which we have referred you. This prospectus, any applicable supplement to this prospectus or any related free writing prospectus do not constitute an offer to sell or the solicitation of an offer to buy any securities other than the registered securities to which they relate, nor do this prospectus, any applicable supplement to this prospectus or any related free writing prospectus constitute an offer to sell or the solicitation of an offer to buy securities in any jurisdiction to any person to whom it is unlawful to make such offer or solicitation in such jurisdiction.

You should not assume that the information contained in this prospectus, any applicable prospectus supplement or any related free writing prospectus is accurate on any date subsequent to the date set forth on the front of the document or that any information we have incorporated by reference is correct on any date subsequent to the date of the document incorporated by reference, even though this prospectus, any applicable prospectus supplement or any related free writing prospectus is delivered, or securities are sold, on a later date.

This prospectus contains summaries of certain provisions contained in some of the documents described herein, but reference is made to the actual documents for complete information. All of the summaries are qualified in their entirety by the actual documents. Copies of some of the documents referred to herein have been filed, will be filed or will be incorporated by reference as exhibits to the registration statement of which this prospectus is a part, and you may obtain copies of those documents as described below under the heading "Where You Can Find More Information."

ii<br>

------

#### **TABLE OF CONTENTS**

#### PROSPECTUS SUMMARY
*This summary highlights selected information from this prospectus and does not contain all of the information that you need to consider in making your investment decision. You should carefully read the entire prospectus, the applicable prospectus supplement and any related free writing prospectus, including the risks of investing in our securities discussed under the heading "Risk Factors" contained herein, in any applicable prospectus supplement and any related free writing prospectus, and under similar headings in the other documents that are incorporated by reference into this prospectus. You should also carefully read the information incorporated by reference into this prospectus, including our financial statements, and the exhibits to the registration statement of which this prospectus is a part. Unless the context requires otherwise, references in this prospectus to "Bionano," "we," "us" and "our" refer to Bionano Genomics, Inc. and its subsidiaries or, as the context may require, Bionano Genomics, Inc. only. "Bionano Laboratories," "BioDiscovery" and "Purigen" refer to our wholly owned subsidiaries, Lineagen, Inc. (doing business as Bionano Laboratories), BioDiscovery, LLC and Purigen Biosystems, Inc., respectively.*

#### Company Overview
We are a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. Our mission is to transform the way the world sees the genome through optical genome mapping, or OGM, solutions, diagnostic services and software. We offer OGM solutions, including our Saphyr system, for applications across basic, translational and clinical research, and for other applications including cell bioprocessing quality control. Through our Bionano Laboratories business, we also provide diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through our BioDiscovery business, we offer an industry-leading, platform-agnostic software solution, our NxClinical software, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. Through our Purigen business, we offer nucleic acid extraction and purification solutions using proprietary isotachophoresis technology, through our Ionic Purification system.

#### Corporate Information
We were formed in January 2003 as BioNanomatrix LLC, a Delaware limited liability company. In August 2007, we became BioNanomatrix Inc., a Delaware corporation. In October 2011, we changed our name to BioNano Genomics, Inc., and in July 2018, we changed our name to Bionano Genomics, Inc.

Our principal executive offices are located at 9540 Towne Centre Drive, Suite 100, San Diego, California 92121, and our telephone number is (858) 888-7600. Our website address is www.bionanogenomics.com and we regularly post copies of our press releases as well as additional information about us on our website. Information contained in, or that can be accessed through, our website is not incorporated by reference into this prospectus and any accompanying prospectus supplement, and you should not consider information on our website to be part of this prospectus or in deciding whether to purchase our securities.

Our design logo, "Bionano," and our other registered and common law trade names, trademarks and service marks are the property of Bionano Genomics, Inc. The trademarks, trade names and service marks appearing in this prospectus and any accompanying prospectus supplement are the property of their respective owners. We do not intend our use or display of other companies' trademarks, trade names or service marks to imply a relationship with, or endorsement or sponsorship of us by, any other companies or products.

1<br>

------

#### **TABLE OF CONTENTS**

#### The Securities We May Offer
We may offer shares of our common stock and preferred stock, various series of debt securities and warrants to purchase any of such securities, up to a total aggregate amount of $400,000,000, either individually or in combination with other securities, from time to time in one or more offerings under this prospectus, together with the applicable prospectus supplement and any related free writing prospectus, at prices and on terms to be determined by market conditions at the time of the relevant offering. This prospectus provides you with a general description of the securities we may offer. Each time we offer a type or series of securities under this prospectus, we will provide a prospectus supplement that will describe the specific amounts, prices and other important terms of the securities, including, to the extent applicable:

&nbsp;&nbsp;&nbsp;&nbsp;• designation or classification;

&nbsp;&nbsp;&nbsp;&nbsp;• aggregate principal amount or aggregate offering price;

&nbsp;&nbsp;&nbsp;&nbsp;• maturity, if applicable;

&nbsp;&nbsp;&nbsp;&nbsp;• original issue discount, if any;

&nbsp;&nbsp;&nbsp;&nbsp;• rates and times of payment of interest or dividends, if any;

&nbsp;&nbsp;&nbsp;&nbsp;• redemption, conversion, exercise, exchange or sinking fund terms, if any;

&nbsp;&nbsp;&nbsp;&nbsp;• conversion or exchange prices or rates, if any, and, if applicable, any provisions for changes to or adjustments in the conversion or exchange prices or rates and in the securities or other property receivable upon conversion or exchange;

&nbsp;&nbsp;&nbsp;&nbsp;• ranking, if applicable;

&nbsp;&nbsp;&nbsp;&nbsp;• restrictive covenants, if any;

&nbsp;&nbsp;&nbsp;&nbsp;• voting or other rights, if any; and

&nbsp;&nbsp;&nbsp;&nbsp;• important U.S. federal income tax considerations.

The prospectus supplement and any related free writing prospectus that we may authorize to be provided to you may also add, update or change information contained in this prospectus or in documents we have incorporated by reference. However, no prospectus supplement or free writing prospectus will offer a security that is not registered and described in this prospectus at the time of the effectiveness of the registration statement of which this prospectus is a part.

#### This prospectus may not be used to consummate a sale of securities unless it is accompanied by a prospectus supplement.
We may sell the securities directly to investors or through underwriters, dealers or agents. We, and our underwriters or agents, reserve the right to accept or reject all or part of any proposed purchase of securities. If we do offer securities through underwriters or agents, we will include in the applicable prospectus supplement:

&nbsp;&nbsp;&nbsp;&nbsp;• the names of those underwriters or agents;

&nbsp;&nbsp;&nbsp;&nbsp;• applicable fees, discounts and commissions to be paid to them;

&nbsp;&nbsp;&nbsp;&nbsp;• details regarding options to purchase additional securities, if any; and

&nbsp;&nbsp;&nbsp;&nbsp;• the estimated net proceeds to us.

***Common Stock. We may issue shares of our common stock from time to time. Holders of our common stock are entitled to one vote per share for the election of directors and on all other matters that require stockholder approval. Subject to any preferential rights of any then outstanding preferred stock, in the event of our liquidation, dissolution or winding up, holders of our common stock are entitled to share ratably in the assets remaining after payment of liabilities and the liquidation preferences of any then outstanding preferred stock. Our common stock does not carry any preemptive rights enabling a holder to subscribe for, or receive shares of, any class of our common stock or any other securities convertible into shares of any class of our common stock, or any redemption rights.***

***Preferred Stock. We may issue shares of our preferred stock from time to time, in one or more series. Under our amended and restated certificate of incorporation, as amended, our board of directors has the authority, without***

2<br>

------

#### **TABLE OF CONTENTS**
further action by stockholders, to designate up to 10,000,000 shares of preferred stock in one or more series and to fix the rights, preferences, privileges, qualifications and restrictions granted to or imposed upon the preferred stock, including dividend rights, conversion rights, voting rights, rights and terms of redemption, liquidation preference and sinking fund terms, any or all of which may be greater than the rights of the common stock. To date, none of the 10,000,000 authorized shares of preferred stock have been designated by our board of directors. Convertible preferred stock will be convertible into our common stock or exchangeable for our other securities. Conversion may be mandatory or at the option of the holders of our preferred stock and would be at prescribed conversion rates.

We will fix the rights, preferences, privileges, qualifications and restrictions of the preferred stock of each series that we sell under this prospectus and applicable prospectus supplements in the certificate of designation relating to that series. We will incorporate by reference into the registration statement of which this prospectus is a part the form of any certificate of designation that describes the terms of the series of preferred stock we are offering before the issuance of the related series of preferred stock. We urge you to read the applicable prospectus supplement (and any related free writing prospectus that we may authorize to be provided to you) related to the series of preferred stock being offered, as well as the complete certificate of designation that contains the terms of the applicable series of preferred stock.

***Debt Securities. We may issue debt securities from time to time, in one or more series, as either senior or subordinated debt or as senior or subordinated convertible debt. The senior debt securities will rank equally with any other unsecured and unsubordinated debt. The subordinated debt securities will be subordinate and junior in right of payment, to the extent and in the manner described in the instrument governing the debt, to all of our senior indebtedness. Convertible debt securities will be convertible into our common stock or preferred stock. Conversion may be mandatory or at the holder's option and would be at prescribed conversion rates.***

The debt securities will be issued under one or more documents called indentures, which are contracts between us and a national banking association or other eligible party, as trustee. In this prospectus, we have summarized certain general features of the debt securities. We urge you, however, to read the applicable prospectus supplement (and any free writing prospectus that we may authorize to be provided to you) related to the series of debt securities being offered, as well as the complete indentures that contain the terms of the debt securities. A form of indenture has been filed as an exhibit to the registration statement of which this prospectus is a part, and supplemental indentures and forms of debt securities containing the terms of the debt securities being offered will be filed as exhibits to the registration statement of which this prospectus is a part or will be incorporated by reference from reports that we file with the SEC.

***Warrants. We may issue warrants for the purchase of common stock, preferred stock and/or debt securities in one or more series. We may issue warrants independently or together with common stock, preferred stock and/or debt securities, and the warrants may be attached to or separate from these securities. In this prospectus, we have summarized certain general features of the warrants. We urge you, however, to read the applicable prospectus supplement (and any free writing prospectus that we may authorize to be provided to you) related to the particular series of warrants being offered, as well as the complete warrant agreements and warrant certificates that contain the terms of the warrants. Forms of the warrant agreements and forms of warrant certificates containing the terms of the warrants being offered have been filed as exhibits to the registration statement of which this prospectus is a part, and supplemental warrant agreements and forms of warrant certificates will be filed as exhibits to the registration statement of which this prospectus is a part or will be incorporated by reference from reports that we file with the SEC.***

We will evidence each series of warrants by warrant certificates that we will issue. Warrants may be issued under an applicable warrant agreement that we enter into with a warrant agent. We will indicate the name and address of the warrant agent, if applicable, in the prospectus supplement relating to the particular series of warrants being offered.

#### Use of Proceeds
Except as described in the applicable prospectus supplement or in any free writing prospectuses we have authorized for use in connection with a specific offering, we currently intend to use the net proceeds from the sale of the securities offered hereby for general corporate purposes, which may include clinical trial and other research and development expenses, capital expenditures, working capital and general and administrative expenses. We may also use a portion of the net proceeds to acquire or invest in businesses, products and technologies that are complementary to our own, although we have no current plans, commitments or agreements with respect to any

3<br>

------

#### **TABLE OF CONTENTS**
acquisitions as of the date of this prospectus. We will set forth in the applicable prospectus supplement or free writing prospectus our intended use for the net proceeds received from the sale of any securities sold pursuant to the prospectus supplement or free writing prospectus. Pending these uses, we intend to invest the net proceeds primarily in money market mutual funds, obligations of the U.S. government and its agencies, money market instruments including commercial paper and negotiable certificates of deposit and corporate bonds. See "Use of Proceeds" in this prospectus for additional information.

#### Risk Factor Summary
*Below is a summary of the principal factors that make an investment in our securities speculative or risky. This summary does not address all of the risks that we face. Additional discussion of the risks and uncertainties summarized in this risk factor summary, and other risks and uncertainties that we face, are set forth below under the heading "Risk Factors" contained in the applicable prospectus supplement and in any free writing prospectuses we have authorized for use in connection with a specific offering, and under similar headings in the documents that are incorporated by reference into this prospectus.*

&nbsp;&nbsp;&nbsp;&nbsp;• We are an early commercial-stage company and have a limited commercial history, which may make it difficult to evaluate our current business and predict our future performance;

&nbsp;&nbsp;&nbsp;&nbsp;• We have incurred recurring net losses since we were formed and expect to incur losses in the future. We cannot be certain that we will achieve or sustain profitability;

&nbsp;&nbsp;&nbsp;&nbsp;• Our quarterly and annual operating results and cash flows have fluctuated in the past and might continue to fluctuate, which makes our future operating results difficult to predict and could cause the market price of our securities to decline substantially;

&nbsp;&nbsp;&nbsp;&nbsp;• Our future capital needs are uncertain and we may require additional funding in the future to advance the commercialization of our Saphyr system, Ionic Purification system, NxClinical software, and our other products, technologies and services, as well as continue our research and development efforts. If we fail to obtain additional funding, we will be forced to delay, reduce or eliminate our commercialization and development efforts;

&nbsp;&nbsp;&nbsp;&nbsp;• Unfavorable geopolitical and macroeconomic developments could adversely affect our business, financial condition or results of operations;

&nbsp;&nbsp;&nbsp;&nbsp;• The COVID-19 pandemic has materially affected and could continue to materially affect our operations globally, including at our headquarters in San Diego, California, as well as the business or operations of our research partners, customers and other third parties with whom we conduct business;

&nbsp;&nbsp;&nbsp;&nbsp;• Acquisitions, joint ventures and other strategic transactions could disrupt or otherwise harm our business and may cause dilution to our stockholders;

&nbsp;&nbsp;&nbsp;&nbsp;• If our products or technologies fail to achieve and sustain sufficient market acceptance, our revenue will be adversely affected;

&nbsp;&nbsp;&nbsp;&nbsp;• In the near term, sales of our Saphyr system, Ionic Purification system, NxClinical software, consumables and genome analysis services will depend on levels of research and development spending by clinical research laboratories, academic and governmental research institutions and biopharmaceutical companies, a reduction in which could limit demand for our technologies and products and adversely affect our business and operating results;

&nbsp;&nbsp;&nbsp;&nbsp;• If we do not successfully manage the development and launch of new products and technologies, our financial results could be adversely affected;

&nbsp;&nbsp;&nbsp;&nbsp;• Our future success is dependent upon our ability to further penetrate our existing customer base, attract new customers and retain the customers of our acquired businesses;

&nbsp;&nbsp;&nbsp;&nbsp;• The size of the markets for our products and technologies may be smaller than we estimate, and new markets may not develop as quickly as we expect, or at all, limiting our ability to successfully sell our products and technologies.

&nbsp;&nbsp;&nbsp;&nbsp;• We are currently limited to "research use only," or RUO, with respect to many of the materials and components used in our consumable products including our assays;

4<br>

------

#### **TABLE OF CONTENTS**
&nbsp;&nbsp;&nbsp;&nbsp;• If the FDA determines that our RUO products are medical devices or if we seek to market our RUO products for clinical diagnostic or health screening use, we will be required to obtain regulatory clearance(s) or approval(s), and may be required to cease or limit sales of our then marketed products, which could materially and adversely affect our business, financial condition and results of operations. Any such regulatory process would be expensive, time-consuming and uncertain both in timing and in outcome;

&nbsp;&nbsp;&nbsp;&nbsp;• If we are unable to protect our intellectual property, it may reduce our ability to maintain any technological or competitive advantage over our competitors and potential competitors, and our business may be harmed; and

&nbsp;&nbsp;&nbsp;&nbsp;• The price of our securities has been and may in the future be volatile or may decline regardless of our operating performance, and you could lose all or part of your investment.

5<br>

------

#### RISK FACTORS
Investing in our securities involves a high degree of risk. Before deciding whether to invest in our securities, you should carefully consider the risks and uncertainties described under the heading "Risk Factors" contained in the applicable prospectus supplement and any related free writing prospectus, and discussed under the heading "Risk Factors" contained in our most recent Annual Report on Form 10-K and in our subsequent Quarterly Reports on Form 10-Q, as well as any amendments thereto reflected in subsequent filings with the SEC, which are incorporated by reference into this prospectus in their entirety, together with other information in this prospectus, the documents incorporated by reference and any free writing prospectus that we may authorize for use in connection with a specific offering. The risks described in these documents are not the only ones we face, but those that we consider to be material factors that make an investment in our common stock speculative or risky. There may be other unknown or unpredictable economic, business, competitive, regulatory or other factors that could have material adverse effects on our future results. Past financial performance may not be a reliable indicator of future performance, and historical trends should not be used to anticipate results or trends in future periods. If any of these risks actually occurs, our business, financial condition, results of operations or cash flow could be seriously harmed. This could cause the trading price of our securities to decline, resulting in a loss of all or part of your investment. Please also carefully read the section below entitled "Special Note Regarding Forward-Looking Statements."

6<br>

------

#### **TABLE OF CONTENTS**

#### SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS
This prospectus and any accompanying prospectus supplement, as well as the documents incorporated by reference in this prospectus or any accompanying prospectus supplement, contain "forward-looking statements" within the meaning of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act. These statements relate to future events or to our future operating or financial performance and involve known and unknown risks, uncertainties and other factors that may cause our actual results, performance or achievements to be materially different from any future results, performances or achievements expressed or implied by the forward-looking statements. Within the meaning of Section 27A of the Securities Act and Section 21E of the Exchange Act, these forward-looking statements may include, but are not limited to, statements about:

&nbsp;&nbsp;&nbsp;&nbsp;• the size and growth potential of the markets for our products, and our ability to serve those markets;

&nbsp;&nbsp;&nbsp;&nbsp;• the rate and degree of market acceptance of our products;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to manage the growth of our business and integrate acquired businesses;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to expand our commercial organization to address effectively existing and new markets that we intend to target;

&nbsp;&nbsp;&nbsp;&nbsp;• the impact from future regulatory, judicial, and legislative changes or developments in the U.S. and foreign countries;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to successfully execute our strategy and meet anticipated goals and milestones;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to compete effectively in a competitive industry;

&nbsp;&nbsp;&nbsp;&nbsp;• the introduction of competitive technologies or improvements in existing technologies and the success of any such technologies;

&nbsp;&nbsp;&nbsp;&nbsp;• the performance of our third-party contract sales organizations, suppliers and manufacturers;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to attract and retain key scientific or management personnel;

&nbsp;&nbsp;&nbsp;&nbsp;• the accuracy of our estimates regarding expenses, future revenues, reimbursement rates, capital requirements and needs for additional financing;

&nbsp;&nbsp;&nbsp;&nbsp;• the impact of geopolitical and macroeconomic developments, such as the ongoing conflict between Ukraine and Russia, related sanctions and the COVID-19 pandemic on our business and operations, as well as the business or operations of our suppliers, customers, manufacturers, research partners and other third parties with whom we conduct business and our expectations with respect to the duration of such impacts and the resulting effects on our business;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to realize the anticipated benefits and synergies of our recent and any future acquisitions or other strategic transactions;

&nbsp;&nbsp;&nbsp;&nbsp;• our intended use of the net proceeds from offerings of our securities under this prospectus;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to continue as a going concern within 12 months from the date of our Annual Report on Form 10-K for the year ended December 31, 2022 and our ability to obtain funding for our operations; and

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to attract collaborators and strategic partnerships.

In some cases, you can identify forward-looking statements by terms such as "anticipates," "believes," "could," "estimates," "expects," "may," "plans," "potential," "predicts," "projects," "should," "would," "will" and similar expressions intended to identify forward-looking statements. These statements reflect our current views with respect to future events, are based on assumptions and are subject to risks and uncertainties. Given these risks and uncertainties, you should not place undue reliance on these forward-looking statements. We discuss in greater detail, and incorporate by reference into the registration statement of which this prospectus is a part in their entirety, many of these risks and uncertainties under the heading "Risk Factors" contained in the applicable prospectus supplement, in any free writing prospectus we may authorize for use in connection with a specific offering, and in our most recent Annual Report on Form 10-K and in our subsequent Quarterly Reports on Form 10-Q, as well as any amendments thereto reflected in subsequent filings with the SEC. Also, these forward-looking statements represent our estimates and assumptions only as of the date of the document containing the applicable statement.

7<br>

------

#### **TABLE OF CONTENTS**
Unless required by law, we undertake no obligation to update or revise any forward-looking statements to reflect new information or future events or developments. Thus, you should not assume that our silence over time means that actual events are bearing out as expressed or implied in such forward-looking statements. You should read this prospectus, the applicable prospectus supplement, together with the documents we have filed with the SEC that are incorporated by reference and any free writing prospectus we have authorized for use in connection with a specific offering completely and with the understanding that our actual future results may be materially different from what we expect. We qualify all of the forward-looking statements in the foregoing documents by these cautionary statements.

8<br>

------

#### USE OF PROCEEDS
We will retain broad discretion over the use of the net proceeds from the sale of the securities offered hereby. Except as described in any prospectus supplement or any related free writing prospectus that we may authorize to be provided to you, we currently intend to use the net proceeds from the sale of the securities offered hereby for general corporate purposes, which may include clinical trial and other research and development expenses, capital expenditures, working capital and general and administrative expenses. We may also use a portion of the net proceeds to acquire or invest in businesses, products and technologies that are complementary to our own, although we have no current plans, commitments or agreements with respect to any acquisitions as of the date of this prospectus. We will set forth in the applicable prospectus supplement or free writing prospectus our intended use for the net proceeds received from the sale of any securities sold pursuant to the prospectus supplement or free writing prospectus. Pending these uses, we intend to invest the net proceeds primarily in money market mutual funds, obligations of the U.S. government and its agencies, money market instruments including commercial paper and negotiable certificates of deposit and corporate bonds.

9<br>

------

#### **TABLE OF CONTENTS**

#### DESCRIPTION OF CAPITAL STOCK
The following description of our capital stock, certain provisions of our certificate of incorporation and bylaws, and certain provisions of Delaware law are summaries. The following description is not complete and is subject to and qualified in its entirety by our certificate of incorporation and bylaws, which are filed as exhibits to the registration statement of which this prospectus is a part, as well as the relevant provisions of the General Corporation Law of the State of Delaware.

As of the date of this prospectus, our certificate of incorporation authorized us to issue 400,000,000 shares of common stock, par value $0.0001 per share, and 10,000,000 shares of preferred stock, par value $0.0001 per share.

#### Common Stock

#### Voting Rights
Our common stock is entitled to one vote for each share held of record on all matters submitted to a vote of the stockholders, including the election of directors, and does not have cumulative voting rights. Our amended and restated certificate of incorporation, as amended, establishes a classified board of directors that is divided into three classes with staggered three-year terms. Only the directors in one class will be subject to election by a plurality of the votes cast at each annual meeting of our stockholders, with the directors in the other classes continuing for the remainder of their respective three-year terms.

#### Economic Rights
Except as otherwise expressly provided in our certificate of incorporation or required by applicable law, all shares of common stock have the same rights and privileges and rank equally, share ratably, and are identical in all respects for all matters, including those described below.

*Dividends. Subject to preferences that may be applicable to any then-outstanding preferred stock, the holders of common stock are entitled to receive dividends, if any, as may be declared from time to time by our board of directors out of legally available funds.*

*Liquidation Rights. In the event of our liquidation, dissolution or winding-up, holders of our common stock are entitled to share ratably in the net assets legally available for distribution to stockholders after the payment of all of our debts and other liabilities, subject to the satisfaction of any liquidation preference granted to the holders of any outstanding shares of preferred stock.*

#### No Preemptive or Similar Rights
The holders of our shares of common stock are not entitled to preemptive rights, and are not subject to conversion, redemption or sinking fund provisions. The rights, preferences and privileges of the holders of our common stock are subject to, and may be adversely affected by, the rights of the holders of shares of any series of our preferred stock that we may designate and issue in the future.

#### Preferred Stock
Our board of directors may authorize the issuance of preferred stock with voting or conversion rights that could adversely affect the voting power or other rights of the holders of the common stock. The issuance of preferred stock, while providing flexibility in connection with possible acquisitions and other corporate purposes, could, among other things, have the effect of delaying, deferring or preventing a change in our control that may otherwise benefit holders of our common stock and may adversely affect the market price of the common stock and the voting and other rights of the holders of common stock. We have no current plans to issue any shares of preferred stock.

10<br>

------

#### **TABLE OF CONTENTS**

#### Anti-Takeover Provisions
We are subject to Section 203 of the General Corporation Law of the State of Delaware. Section 203 generally prohibits a public Delaware corporation from engaging in a "business combination" with an "interested stockholder" for a period of three years after the date of the transaction in which the person became an interested stockholder, unless:

&nbsp;&nbsp;&nbsp;&nbsp;• prior to the date of the transaction, the board of directors of the corporation approved either the business combination or the transaction which resulted in the stockholder becoming an interested stockholder;

&nbsp;&nbsp;&nbsp;&nbsp;• upon consummation of the transaction which resulted in the stockholder becoming an interested stockholder, the interested stockholder owned at least 85% of the voting stock of the corporation outstanding at the commencement of the transaction, excluding for purposes of determining the number of shares outstanding (but not the outstanding voting stock owned by the interested stockholder) (a) shares owned by persons who are directors and also officers and (b) shares owned by employee stock plans in which employee participants do not have the right to determine confidentially whether shares held subject to the plan will be tendered in a tender or exchange offer; or

&nbsp;&nbsp;&nbsp;&nbsp;• on or subsequent to the consummation of the transaction, the business combination is approved by the board of directors and authorized at an annual or special meeting of stockholders, and not by written consent, by the affirmative vote of at least 66 2/3% of the outstanding voting stock which is not owned by the interested stockholder.

Section 203 of the DGCL defines a business combination to include:

&nbsp;&nbsp;&nbsp;&nbsp;• any merger or consolidation involving the corporation and the interested stockholder;

&nbsp;&nbsp;&nbsp;&nbsp;• any sale, lease, exchange, mortgage, pledge, transfer or other disposition involving the interested stockholder of 10% or more of the assets of the corporation;

&nbsp;&nbsp;&nbsp;&nbsp;• subject to exceptions, any transaction involving the corporation that has the effect of increasing the proportionate share of the stock of any class or series of the corporation beneficially owned by the interested stockholder;

&nbsp;&nbsp;&nbsp;&nbsp;• subject to exceptions, any transaction that results in the issuance or transfer by the corporation of any stock of the corporation to the interested stockholder; and

&nbsp;&nbsp;&nbsp;&nbsp;• the receipt by the interested stockholder of the benefit of any loans, advances, guarantees, pledges or other financial benefits provided by or through the corporation.

In general, Section 203 defines an interested stockholder as any entity or person beneficially owning 15% or more of the outstanding voting stock of the corporation and any entity or person affiliated with or controlling or controlled by the entity or person.

#### Certificate of Incorporation and Bylaws to be in Effect upon the Closing of this Offering
Among other things, our amended and restated certificate of incorporation, as amended, and amended and restated bylaws:

&nbsp;&nbsp;&nbsp;&nbsp;• do not provide stockholders with cumulative voting rights such that stockholders holding a majority of the voting power of our shares of common stock may be able to elect all of our directors;

&nbsp;&nbsp;&nbsp;&nbsp;• provide for stockholder actions to be taken at a duly called meeting of stockholders and not by written consent;

&nbsp;&nbsp;&nbsp;&nbsp;• provide that a special meeting of stockholders may only be called by a majority of our board of directors, the chair of our board of directors or our chief executive officer;

&nbsp;&nbsp;&nbsp;&nbsp;• establish an advance notice procedure for stockholder proposals to be brought before an annual meeting of our stockholders, including proposed nominations of persons for election to our board of directors;

&nbsp;&nbsp;&nbsp;&nbsp;• divide our board of directors into three classes with staggered three-year terms;

&nbsp;&nbsp;&nbsp;&nbsp;• provide that the authorized number of directors may be changed only by resolution adopted by a majority of the authorized number of directors constituting the board of directors;

11<br>

------

#### **TABLE OF CONTENTS**
&nbsp;&nbsp;&nbsp;&nbsp;• provide that the board of directors or any individual director may only be removed with cause and the affirmative vote of the holders of at least 66 2/3% of the voting power of all of our then outstanding common stock;

&nbsp;&nbsp;&nbsp;&nbsp;• provide that all vacancies, including newly created directorships, may, except as otherwise required by law or subject to the rights of holders of preferred stock as designated from time to time, be filled by the affirmative vote of a majority of directors then in office, even if less than a quorum;

The foregoing provisions make it difficult for another party to obtain control of us by replacing our board of directors. Since our board of directors has the power to retain and discharge our officers, these provisions could also make it more difficult for existing stockholders or another party to effect a change in management. In addition, the authorization of undesignated preferred stock makes it possible for our board of directors to issue preferred stock with voting or other rights or preferences that could impede the success of any attempt to change our control.

These provisions are designed to reduce our vulnerability to an unsolicited acquisition proposal and to discourage certain tactics that may be used in proxy fights. However, such provisions could have the effect of discouraging others from making tender offers for our shares and may have the effect of deterring hostile takeovers or delaying changes in our control or management. As a consequence, these provisions may also inhibit fluctuations in the market price of our stock that could result from actual or rumored takeover attempts.

#### Section 203 of the General Corporation Law of the State of Delaware
We are subject to Section 203 of the General Corporation Law of the State of Delaware, which prohibits a Delaware corporation from engaging in any business combination with any interested stockholder for a period of three years after the date that such stockholder became an interested stockholder, subject to certain exceptions.

#### Transfer Agent and Registrar
Our transfer agent and registrar for our common stock is American Stock Transfer & Trust Company, LLC. The transfer agent for any series of preferred stock that we may offer under this prospectus will be named and described in the prospectus supplement related to that series.

#### Listing on the Nasdaq Capital Market
Our common stock is listed on the Nasdaq Capital Market under the symbol "BNGO." The applicable prospectus supplement will contain information, where applicable, as to any other listing, if any, on the Nasdaq Capital Market or any securities market or other exchange of the preferred stock covered by such prospectus supplement.

12<br>

------

#### **TABLE OF CONTENTS**

#### DESCRIPTION OF DEBT SECURITIES
We may issue debt securities from time to time, in one or more series, as either senior or subordinated debt or as senior or subordinated convertible debt. While the terms we have summarized below will apply generally to any debt securities that we may offer under this prospectus, we will describe the particular terms of any debt securities that we may offer in more detail in the applicable prospectus supplement. The terms of any debt securities offered under a prospectus supplement may differ from the terms described below. Unless the context requires otherwise, whenever we refer to the indenture, we also are referring to any supplemental indentures that specify the terms of a particular series of debt securities.

We will issue the debt securities under the indenture that we will enter into with the trustee named in the indenture. The indenture will be qualified under the Trust Indenture Act of 1939, as amended, or the Trust Indenture Act. We have filed the form of indenture as an exhibit to the registration statement of which this prospectus is a part, and supplemental indentures and forms of debt securities containing the terms of the debt securities being offered will be filed as exhibits to the registration statement of which this prospectus is a part or will be incorporated by reference from reports that we file with the SEC.

The following summary of material provisions of the debt securities and the indenture is subject to, and qualified in its entirety by reference to, all of the provisions of the indenture applicable to a particular series of debt securities. We urge you to read the applicable prospectus supplements and any related free writing prospectuses related to the debt securities that we may offer under this prospectus, as well as the complete indenture that contains the terms of the debt securities.

#### General
The indenture does not limit the amount of debt securities that we may issue. It provides that we may issue debt securities up to the principal amount that we may authorize and may be in any currency or currency unit that we may designate. Except for the limitations on consolidation, merger and sale of all or substantially all of our assets contained in the indenture, the terms of the indenture do not contain any covenants or other provisions designed to give holders of any debt securities protection against changes in our operations, financial condition or transactions involving us.

We may issue the debt securities issued under the indenture as "discount securities," which means they may be sold at a discount below their stated principal amount. These debt securities, as well as other debt securities that are not issued at a discount, may be issued with "original issue discount," or OID, for U.S. federal income tax purposes because of interest payment and other characteristics or terms of the debt securities. Material U.S. federal income tax considerations applicable to debt securities issued with OID will be described in more detail in any applicable prospectus supplement.

We will describe in the applicable prospectus supplement the terms of the series of debt securities being offered, including:

&nbsp;&nbsp;&nbsp;&nbsp;• the title of the series of debt securities;

&nbsp;&nbsp;&nbsp;&nbsp;• any limit upon the aggregate principal amount that may be issued;

&nbsp;&nbsp;&nbsp;&nbsp;• the maturity date or dates;

&nbsp;&nbsp;&nbsp;&nbsp;• the form of the debt securities of the series;

&nbsp;&nbsp;&nbsp;&nbsp;• the applicability of any guarantees;

&nbsp;&nbsp;&nbsp;&nbsp;• whether or not the debt securities will be secured or unsecured, and the terms of any secured debt;

&nbsp;&nbsp;&nbsp;&nbsp;• whether the debt securities rank as senior debt, senior subordinated debt, subordinated debt or any combination thereof, and the terms of any subordination;

&nbsp;&nbsp;&nbsp;&nbsp;• if the price (expressed as a percentage of the aggregate principal amount thereof) at which such debt securities will be issued is a price other than the principal amount thereof, the portion of the principal amount thereof payable upon declaration of acceleration of the maturity thereof, or if applicable, the portion of the principal amount of such debt securities that is convertible into another security or the method by which any such portion shall be determined;

13<br>

------

#### **TABLE OF CONTENTS**
&nbsp;&nbsp;&nbsp;&nbsp;• the interest rate or rates, which may be fixed or variable, or the method for determining the rate and the date interest will begin to accrue, the dates interest will be payable and the regular record dates for interest payment dates or the method for determining such dates;

&nbsp;&nbsp;&nbsp;&nbsp;• our right, if any, to defer payment of interest and the maximum length of any such deferral period;

&nbsp;&nbsp;&nbsp;&nbsp;• if applicable, the date or dates after which, or the period or periods during which, and the price or prices at which, we may, at our option, redeem the series of debt securities pursuant to any optional or provisional redemption provisions and the terms of those redemption provisions;

&nbsp;&nbsp;&nbsp;&nbsp;• the date or dates, if any, on which, and the price or prices at which we are obligated, pursuant to any mandatory sinking fund or analogous fund provisions or otherwise, to redeem, or at the holder's option to purchase, the series of debt securities and the currency or currency unit in which the debt securities are payable;

&nbsp;&nbsp;&nbsp;&nbsp;• the denominations in which we will issue the series of debt securities, if other than denominations of $1,000 and any integral multiple thereof;

&nbsp;&nbsp;&nbsp;&nbsp;• any and all terms, if applicable, relating to any auction or remarketing of the debt securities of that series and any security for our obligations with respect to such debt securities and any other terms which may be advisable in connection with the marketing of debt securities of that series;

&nbsp;&nbsp;&nbsp;&nbsp;• whether the debt securities of the series shall be issued in whole or in part in the form of a global security or securities; the terms and conditions, if any, upon which such global security or securities may be exchanged in whole or in part for other individual securities; and the depositary for such global security or securities;

&nbsp;&nbsp;&nbsp;&nbsp;• if applicable, the provisions relating to conversion or exchange of any debt securities of the series and the terms and conditions upon which such debt securities will be so convertible or exchangeable, including the conversion or exchange price, as applicable, or how it will be calculated and may be adjusted, any mandatory or optional (at our option or the holders' option) conversion or exchange features, the applicable conversion or exchange period and the manner of settlement for any conversion or exchange;

&nbsp;&nbsp;&nbsp;&nbsp;• if other than the full principal amount thereof, the portion of the principal amount of debt securities of the series which shall be payable upon declaration of acceleration of the maturity thereof;

&nbsp;&nbsp;&nbsp;&nbsp;• additions to or changes in the covenants applicable to the particular debt securities being issued, including, among others, the consolidation, merger or sale covenant;

&nbsp;&nbsp;&nbsp;&nbsp;• additions to or changes in the events of default with respect to the securities and any change in the right of the trustee or the holders to declare the principal, premium, if any, and interest, if any, with respect to such securities to be due and payable;

&nbsp;&nbsp;&nbsp;&nbsp;• additions to or changes in or deletions of the provisions relating to covenant defeasance and legal defeasance;

&nbsp;&nbsp;&nbsp;&nbsp;• additions to or changes in the provisions relating to satisfaction and discharge of the indenture;

&nbsp;&nbsp;&nbsp;&nbsp;• additions to or changes in the provisions relating to the modification of the indenture both with and without the consent of holders of debt securities issued under the indenture;

&nbsp;&nbsp;&nbsp;&nbsp;• the currency of payment of debt securities if other than U.S. dollars and the manner of determining the equivalent amount in U.S. dollars;

&nbsp;&nbsp;&nbsp;&nbsp;• whether interest will be payable in cash or additional debt securities at our or the holders' option and the terms and conditions upon which the election may be made;

&nbsp;&nbsp;&nbsp;&nbsp;• the terms and conditions, if any, upon which we will pay amounts in addition to the stated interest, premium, if any and principal amounts of the debt securities of the series to any holder that is not a "United States person" for federal tax purposes;

&nbsp;&nbsp;&nbsp;&nbsp;• any restrictions on transfer, sale or assignment of the debt securities of the series; and

&nbsp;&nbsp;&nbsp;&nbsp;• any other specific terms, preferences, rights or limitations of, or restrictions on, the debt securities, any other additions or changes in the provisions of the indenture, and any terms that may be required by us or advisable under applicable laws or regulations.

14<br>

------

#### Conversion or Exchange Rights
We will set forth in the applicable prospectus supplement the terms on which a series of debt securities may be convertible into or exchangeable for our common stock or our other securities. We will include provisions as to settlement upon conversion or exchange and whether conversion or exchange is mandatory, at the option of the holder or at our option. We may include provisions pursuant to which the number of shares of our common stock or our other securities that the holders of the series of debt securities receive would be subject to adjustment.

#### Consolidation, Merger or Sale
Unless we provide otherwise in the prospectus supplement applicable to a particular series of debt securities, the indenture will not contain any covenant that restricts our ability to merge or consolidate, or sell, convey, transfer or otherwise dispose of our assets as an entirety or substantially as an entirety. However, any successor to or acquirer of such assets (other than a subsidiary of ours) must assume all of our obligations under the indenture or the debt securities, as appropriate.

#### Events of Default under the Indenture
Unless we provide otherwise in the prospectus supplement applicable to a particular series of debt securities, the following are events of default under the indenture with respect to any series of debt securities that we may issue:

&nbsp;&nbsp;&nbsp;&nbsp;• if we fail to pay any installment of interest on any series of debt securities, as and when the same shall become due and payable, and such default continues for a period of 90 days; provided, however, that a valid extension of an interest payment period by us in accordance with the terms of any indenture supplemental thereto shall not constitute a default in the payment of interest for this purpose;

&nbsp;&nbsp;&nbsp;&nbsp;• if we fail to pay the principal of, or premium, if any, on any series of debt securities as and when the same shall become due and payable whether at maturity, upon redemption, by declaration or otherwise, or in any payment required by any sinking or analogous fund established with respect to such series; provided, however, that a valid extension of the maturity of such debt securities in accordance with the terms of any indenture supplemental thereto shall not constitute a default in the payment of principal or premium, if any;

&nbsp;&nbsp;&nbsp;&nbsp;• if we fail to observe or perform any other covenant or agreement contained in the debt securities or the indenture, other than a covenant specifically relating to another series of debt securities, and our failure continues for 90 days after we receive written notice of such failure, requiring the same to be remedied and stating that such is a notice of default thereunder, from the trustee or holders of at least 25% in aggregate principal amount of the outstanding debt securities of the applicable series; and

&nbsp;&nbsp;&nbsp;&nbsp;• if specified events of bankruptcy, insolvency or reorganization occur.

If an event of default with respect to debt securities of any series occurs and is continuing, other than an event of default specified in the last bullet point above, the trustee or the holders of at least 25% in aggregate principal amount of the outstanding debt securities of that series, by notice to us in writing, and to the trustee if notice is given by such holders, may declare the unpaid principal of, premium, if any, and accrued interest, if any, due and payable immediately. If an event of default specified in the last bullet point above occurs with respect to us, the principal amount of and accrued interest, if any, of each issue of debt securities then outstanding shall be due and payable without any notice or other action on the part of the trustee or any holder.

The holders of a majority in principal amount of the outstanding debt securities of an affected series may waive any default or event of default with respect to the series and its consequences, except defaults or events of default regarding payment of principal, premium, if any, or interest, unless we have cured the default or event of default in accordance with the indenture. Any waiver shall cure the default or event of default.

15<br>

------

#### **TABLE OF CONTENTS**
Subject to the terms of the indenture, if an event of default under an indenture shall occur and be continuing, the trustee will be under no obligation to exercise any of its rights or powers under such indenture at the request or direction of any of the holders of the applicable series of debt securities, unless such holders have offered the trustee reasonable indemnity. The holders of a majority in principal amount of the outstanding debt securities of any series will have the right to direct the time, method and place of conducting any proceeding for any remedy available to the trustee, or exercising any trust or power conferred on the trustee, with respect to the debt securities of that series, provided that:

&nbsp;&nbsp;&nbsp;&nbsp;• the direction so given by the holder is not in conflict with any law or the applicable indenture; and

&nbsp;&nbsp;&nbsp;&nbsp;• subject to its duties under the Trust Indenture Act, the trustee need not take any action that might involve it in personal liability or might be unduly prejudicial to the holders not involved in the proceeding.

A holder of the debt securities of any series will have the right to institute a proceeding under the indenture or to appoint a receiver or trustee, or to seek other remedies only if:

&nbsp;&nbsp;&nbsp;&nbsp;• the holder has given written notice to the trustee of a continuing event of default with respect to that series;

&nbsp;&nbsp;&nbsp;&nbsp;• the holders of at least 25% in aggregate principal amount of the outstanding debt securities of that series have made written request;

&nbsp;&nbsp;&nbsp;&nbsp;• such holders have offered to the trustee indemnity satisfactory to it against the costs, expenses and liabilities to be incurred by the trustee in compliance with the request; and

&nbsp;&nbsp;&nbsp;&nbsp;• the trustee does not institute the proceeding, and does not receive from the holders of a majority in aggregate principal amount of the outstanding debt securities of that series other conflicting directions within 90 days after the notice, request and offer.

These limitations do not apply to a suit instituted by a holder of debt securities if we default in the payment of the principal, premium, if any, or interest on, the debt securities.

We will periodically file statements with the trustee regarding our compliance with specified covenants in the indenture.

#### Modification of Indenture; Waiver
We and the trustee may change an indenture without the consent of any holders with respect to specific matters:

&nbsp;&nbsp;&nbsp;&nbsp;• to cure any ambiguity, defect or inconsistency in the indenture or in the debt securities of any series;

&nbsp;&nbsp;&nbsp;&nbsp;• to comply with the provisions described above under "Description of Debt Securities—Consolidation, Merger or Sale;"

&nbsp;&nbsp;&nbsp;&nbsp;• to provide for uncertificated debt securities in addition to or in place of certificated debt securities;

&nbsp;&nbsp;&nbsp;&nbsp;• to add to our covenants, restrictions, conditions or provisions such new covenants, restrictions, conditions or provisions for the benefit of the holders of all or any series of debt securities, to make the occurrence, or the occurrence and the continuance, of a default in any such additional covenants, restrictions, conditions or provisions an event of default or to surrender any right or power conferred upon us in the indenture;

&nbsp;&nbsp;&nbsp;&nbsp;• to add to, delete from or revise the conditions, limitations, and restrictions on the authorized amount, terms, or purposes of issue, authentication and delivery of debt securities, as set forth in the indenture;

&nbsp;&nbsp;&nbsp;&nbsp;• to make any change that does not adversely affect the interests of any holder of debt securities of any series in any material respect;

&nbsp;&nbsp;&nbsp;&nbsp;• to provide for the issuance of and establish the form and terms and conditions of the debt securities of any series as provided above under "Description of Debt Securities—General" to establish the form of any certifications required to be furnished pursuant to the terms of the indenture or any series of debt securities, or to add to the rights of the holders of any series of debt securities;

&nbsp;&nbsp;&nbsp;&nbsp;• to evidence and provide for the acceptance of appointment under any indenture by a successor trustee; or

&nbsp;&nbsp;&nbsp;&nbsp;• to comply with any requirements of the SEC in connection with the qualification of any indenture under the Trust Indenture Act.

16<br>

------

#### **TABLE OF CONTENTS**
In addition, under the indenture, the rights of holders of a series of debt securities may be changed by us and the trustee with the written consent of the holders of at least a majority in aggregate principal amount of the outstanding debt securities of each series that is affected. However, unless we provide otherwise in the prospectus supplement applicable to a particular series of debt securities, we and the trustee may make the following changes only with the consent of each holder of any outstanding debt securities affected:

&nbsp;&nbsp;&nbsp;&nbsp;• extending the fixed maturity of any debt securities of any series;

&nbsp;&nbsp;&nbsp;&nbsp;• reducing the principal amount, reducing the rate of or extending the time of payment of interest, or reducing any premium payable upon the redemption of any series of any debt securities; or

&nbsp;&nbsp;&nbsp;&nbsp;• reducing the percentage of debt securities, the holders of which are required to consent to any amendment, supplement, modification or waiver.

#### Discharge
Each indenture provides that we can elect to be discharged from our obligations with respect to one or more series of debt securities, except for specified obligations, including obligations to:

&nbsp;&nbsp;&nbsp;&nbsp;• provide for payment;

&nbsp;&nbsp;&nbsp;&nbsp;• register the transfer or exchange of debt securities of the series;

&nbsp;&nbsp;&nbsp;&nbsp;• replace stolen, lost or mutilated debt securities of the series;

&nbsp;&nbsp;&nbsp;&nbsp;• pay principal of and premium and interest on any debt securities of the series;

&nbsp;&nbsp;&nbsp;&nbsp;• maintain paying agencies;

&nbsp;&nbsp;&nbsp;&nbsp;• hold monies for payment in trust;

&nbsp;&nbsp;&nbsp;&nbsp;• recover excess money held by the trustee;

&nbsp;&nbsp;&nbsp;&nbsp;• compensate and indemnify the trustee; and

&nbsp;&nbsp;&nbsp;&nbsp;• appoint any successor trustee.

In order to exercise our rights to be discharged, we must deposit with the trustee money or government obligations sufficient to pay all the principal of, any premium, if any, and interest on, the debt securities of the series on the dates payments are due.

#### Form, Exchange and Transfer
We will issue the debt securities of each series only in fully registered form without coupons and, unless we provide otherwise in the applicable prospectus supplement, in denominations of $1,000 and any integral multiple thereof. The indenture provides that we may issue debt securities of a series in temporary or permanent global form and as book-entry securities that will be deposited with, or on behalf of, The Depository Trust Company, or DTC, or another depositary named by us and identified in the applicable prospectus supplement with respect to that series. To the extent the debt securities of a series are issued in global form and as book-entry, a description of terms relating to any book-entry securities will be set forth in the applicable prospectus supplement.

At the option of the holder, subject to the terms of the indenture and the limitations applicable to global securities described in the applicable prospectus supplement, the holder of the debt securities of any series can exchange the debt securities for other debt securities of the same series, in any authorized denomination and of like tenor and aggregate principal amount.

Subject to the terms of the indenture and the limitations applicable to global securities set forth in the applicable prospectus supplement, holders of the debt securities may present the debt securities for exchange or for registration of transfer, duly endorsed or with the form of transfer endorsed thereon duly executed if so required by us or the security registrar, at the office of the security registrar or at the office of any transfer agent designated by us for this purpose. Unless otherwise provided in the debt securities that the holder presents for transfer or exchange, we will impose no service charge for any registration of transfer or exchange, but we may require payment of any taxes or other governmental charges.

We will name in the applicable prospectus supplement the security registrar, and any transfer agent in addition to the security registrar, that we initially designate for any debt securities. We may at any time designate additional

17<br>

------

#### **TABLE OF CONTENTS**
transfer agents or rescind the designation of any transfer agent or approve a change in the office through which any transfer agent acts, except that we will be required to maintain a transfer agent in each place of payment for the debt securities of each series.

If we elect to redeem the debt securities of any series, we will not be required to:

&nbsp;&nbsp;&nbsp;&nbsp;• issue, register the transfer of, or exchange any debt securities of that series during a period beginning at the opening of business 15 days before the day of mailing of a notice of redemption of any debt securities that may be selected for redemption and ending at the close of business on the day of the mailing; or

&nbsp;&nbsp;&nbsp;&nbsp;• register the transfer of or exchange any debt securities so selected for redemption, in whole or in part, except the unredeemed portion of any debt securities we are redeeming in part.

#### Information Concerning the Trustee
The trustee, other than during the occurrence and continuance of an event of default under an indenture, undertakes to perform only those duties as are specifically set forth in the applicable indenture. Upon an event of default under an indenture, the trustee must use the same degree of care as a prudent person would exercise or use in the conduct of his or her own affairs. Subject to this provision, the trustee is under no obligation to exercise any of the powers given it by the indenture at the request of any holder of debt securities unless it is offered reasonable security and indemnity against the costs, expenses and liabilities that it might incur.

#### Payment and Paying Agents
Unless we otherwise indicate in the applicable prospectus supplement, we will make payment of the interest on any debt securities on any interest payment date to the person in whose name the debt securities, or one or more predecessor securities, are registered at the close of business on the regular record date for the interest.

We will pay principal of and any premium and interest on the debt securities of a particular series at the office of the paying agents designated by us, except that unless we otherwise indicate in the applicable prospectus supplement, we will make interest payments by check that we will mail to the holder or by wire transfer to certain holders. Unless we otherwise indicate in the applicable prospectus supplement, we will designate the corporate trust office of the trustee as our sole paying agent for payments with respect to debt securities of each series. We will name in the applicable prospectus supplement any other paying agents that we initially designate for the debt securities of a particular series. We will maintain a paying agent in each place of payment for the debt securities of a particular series.

All money we pay to a paying agent or the trustee for the payment of the principal of or any premium or interest on any debt securities that remains unclaimed at the end of two years after such principal, premium or interest has become due and payable will be repaid to us, and the holder of the debt security thereafter may look only to us for payment thereof.

#### Governing Law
The indenture and the debt securities will be governed by and construed in accordance with the internal laws of the State of New York, except to the extent that the Trust Indenture Act is applicable.

18<br>

------

#### **TABLE OF CONTENTS**

#### DESCRIPTION OF WARRANTS
The following description, together with the additional information we may include in any applicable prospectus supplements and free writing prospectuses that we may authorize to be distributed to you, summarizes the material terms and provisions of the warrants that we may offer under this prospectus, which may consist of warrants to purchase common stock, preferred stock or debt securities and may be issued in one or more series. Warrants may be issued independently or together with common stock, preferred stock or debt securities offered by any prospectus supplement, and may be attached to or separate from those securities. While the terms we have summarized below will apply generally to any warrants that we may offer under this prospectus, we will describe the particular terms of any series of warrants that we may offer in more detail in the applicable prospectus supplement and any applicable free writing prospectus. The terms of any warrants offered under a prospectus supplement may differ from the terms described below. However, no prospectus supplement will fundamentally change the terms that are set forth in this prospectus or offer a security that is not registered and described in this prospectus at the time of its effectiveness.

We have filed forms of the warrant agreements and forms of warrant certificates containing the terms of the warrants being offered as exhibits to the registration statement of which this prospectus is a part. We will file as exhibits to the registration statement of which this prospectus is a part, or will incorporate by reference from reports that we file with the SEC, the form of warrant agreement, if any, including a form of warrant certificate, that describes the terms of the particular series of warrants we are offering. The following summaries of material provisions of the warrants and the warrant agreements are subject to, and qualified in their entirety by reference to, all the provisions of the warrant agreement and warrant certificate applicable to the particular series of warrants that we may offer under this prospectus. We urge you to read the applicable prospectus supplements related to the particular series of warrants that we may offer under this prospectus, as well as any related free writing prospectuses, and the complete warrant agreements and warrant certificates that contain the terms of the warrants.

#### General
We will describe in the applicable prospectus supplement the terms relating to a series of warrants being offered, including:

&nbsp;&nbsp;&nbsp;&nbsp;• the title of such securities;

&nbsp;&nbsp;&nbsp;&nbsp;• the offering price or prices and aggregate number of warrants offered;

&nbsp;&nbsp;&nbsp;&nbsp;• the currency or currencies for which the warrants may be purchased;

&nbsp;&nbsp;&nbsp;&nbsp;• if applicable, the designation and terms of the securities with which the warrants are issued and the number of warrants issued with each such security or each principal amount of such security;

&nbsp;&nbsp;&nbsp;&nbsp;• if applicable, the date on and after which the warrants and the related securities will be separately transferable;

&nbsp;&nbsp;&nbsp;&nbsp;• if applicable, the minimum or maximum amount of such warrants which may be exercised at any one time;

&nbsp;&nbsp;&nbsp;&nbsp;• in the case of warrants to purchase debt securities, the principal amount of debt securities purchasable upon exercise of one warrant and the price at which, and currency in which, this principal amount of debt securities may be purchased upon such exercise;

&nbsp;&nbsp;&nbsp;&nbsp;• in the case of warrants to purchase common stock or preferred stock, the number of shares of common stock or preferred stock, as the case may be, purchasable upon the exercise of one warrant and the price at which, and the currency in which, these shares may be purchased upon such exercise;

&nbsp;&nbsp;&nbsp;&nbsp;• the effect of any merger, consolidation, sale or other disposition of our business on the warrant agreements and the warrants;

&nbsp;&nbsp;&nbsp;&nbsp;• the terms of any rights to redeem or call the warrants;

&nbsp;&nbsp;&nbsp;&nbsp;• the terms of any rights to force the exercise of the warrants;

&nbsp;&nbsp;&nbsp;&nbsp;• any provisions for changes to or adjustments in the exercise price or number of securities issuable upon exercise of the warrants;

&nbsp;&nbsp;&nbsp;&nbsp;• the dates on which the right to exercise the warrants will commence and expire;

&nbsp;&nbsp;&nbsp;&nbsp;• the manner in which the warrant agreements and warrants may be modified;

19<br>

------

#### **TABLE OF CONTENTS**
&nbsp;&nbsp;&nbsp;&nbsp;• a discussion of any material or special U.S. federal income tax consequences of holding or exercising the warrants;

&nbsp;&nbsp;&nbsp;&nbsp;• the terms of the securities issuable upon exercise of the warrants; and

&nbsp;&nbsp;&nbsp;&nbsp;• any other specific terms, preferences, rights or limitations of or restrictions on the warrants.

Before exercising their warrants, holders of warrants will not have any of the rights of holders of the securities purchasable upon such exercise, including:

&nbsp;&nbsp;&nbsp;&nbsp;• in the case of warrants to purchase debt securities, the right to receive payments of principal of, or premium, if any, or interest on, the debt securities purchasable upon exercise or to enforce covenants in the applicable indenture; or

&nbsp;&nbsp;&nbsp;&nbsp;• in the case of warrants to purchase common stock or preferred stock, the right to receive dividends, if any, or, payments upon our liquidation, dissolution or winding up or to exercise voting rights, if any.

#### Exercise of Warrants
Each warrant will entitle the holder to purchase the securities that we specify in the applicable prospectus supplement at the exercise price that we describe in the applicable prospectus supplement. Unless we otherwise specify in the applicable prospectus supplement, holders of the warrants may exercise the warrants at any time up to the specified time on the expiration date that we set forth in the applicable prospectus supplement. After the close of business on the expiration date, unexercised warrants will become void.

Unless we otherwise specify in the applicable prospectus supplement, holders of the warrants may exercise the warrants by delivering the warrant certificate representing the warrants to be exercised together with specified information, and paying the required amount to the warrant agent in immediately available funds, as provided in the applicable prospectus supplement. We will set forth on the reverse side of the warrant certificate and in the applicable prospectus supplement the information that the holder of the warrant will be required to deliver to the warrant agent in connection with the exercise of the warrant.

Upon receipt of the required payment and the warrant certificate properly completed and duly executed at the corporate trust office of the warrant agent or any other office indicated in the applicable prospectus supplement, we will issue and deliver the securities purchasable upon such exercise. If fewer than all of the warrants represented by the warrant certificate are exercised, then we will issue a new warrant certificate for the remaining amount of warrants. If we so indicate in the applicable prospectus supplement, holders of the warrants may surrender securities as all or part of the exercise price for warrants.

#### Governing Law
Unless we provide otherwise in the applicable prospectus supplement, the warrants and warrant agreements, and any claim, controversy or dispute arising under or related to the warrants or warrant agreements, will be governed by and construed in accordance with the laws of the State of New York.

#### Enforceability of Rights by Holders of Warrants
Each warrant agent will act solely as our agent under the applicable warrant agreement and will not assume any obligation or relationship of agency or trust with any holder of any warrant. A single bank or trust company may act as warrant agent for more than one issue of warrants. A warrant agent will have no duty or responsibility in case of any default by us under the applicable warrant agreement or warrant, including any duty or responsibility to initiate any proceedings at law or otherwise, or to make any demand upon us. Any holder of a warrant may, without the consent of the related warrant agent or the holder of any other warrant, enforce by appropriate legal action its right to exercise, and receive the securities purchasable upon exercise of, its warrants.

20<br>

------

#### **TABLE OF CONTENTS**

#### LEGAL OWNERSHIP OF SECURITIES
We can issue securities in registered form or in the form of one or more global securities. We describe global securities in greater detail below. We refer to those persons who have securities registered in their own names on the books that we or any applicable trustee or depositary maintain for this purpose as the "holders" of those securities. These persons are the legal holders of the securities. We refer to those persons who, indirectly through others, own beneficial interests in securities that are not registered in their own names, as "indirect holders" of those securities. As we discuss below, indirect holders are not legal holders, and investors in securities issued in book-entry form or in street name will be indirect holders.

#### Book-Entry Holders
We may issue securities in book-entry form only, as we will specify in the applicable prospectus supplement. This means securities may be represented by one or more global securities registered in the name of a financial institution that holds them as depositary on behalf of other financial institutions that participate in the depositary's book-entry system. These participating institutions, which are referred to as participants, in turn, hold beneficial interests in the securities on behalf of themselves or their customers.

Only the person in whose name a security is registered is recognized as the holder of that security. Global securities will be registered in the name of the depositary or its participants. Consequently, for global securities, we will recognize only the depositary as the holder of the securities, and we will make all payments on the securities to the depositary. The depositary passes along the payments it receives to its participants, which in turn pass the payments along to their customers who are the beneficial owners. The depositary and its participants do so under agreements they have made with one another or with their customers; they are not obligated to do so under the terms of the securities.

As a result, investors in a global security will not own securities directly. Instead, they will own beneficial interests in a global security, through a bank, broker or other financial institution that participates in the depositary's book-entry system or holds an interest through a participant. As long as the securities are issued in global form, investors will be indirect holders, and not legal holders, of the securities.

#### Street Name Holders
A global security may be terminated in certain situations as described under "—Special Situations When a Global Security Will Be Terminated," or issue securities that are not issued in global form. In these cases, investors may choose to hold their securities in their own names or in "street name." Securities held by an investor in street name would be registered in the name of a bank, broker or other financial institution that the investor chooses, and the investor would hold only a beneficial interest in those securities through an account he or she maintains at that institution.

For securities held in street name, we or any applicable trustee or depositary will recognize only the intermediary banks, brokers and other financial institutions in whose names the securities are registered as the holders of those securities, and we or any such trustee or depositary will make all payments on those securities to them. These institutions pass along the payments they receive to their customers who are the beneficial owners, but only because they agree to do so in their customer agreements or because they are legally required to do so. Investors who hold securities in street name will be indirect holders, not holders, of those securities.

#### Legal Holders
Our obligations, as well as the obligations of any applicable trustee or third party employed by us or a trustee, run only to the legal holders of the securities. We do not have obligations to investors who hold beneficial interests in global securities, in street name or by any other indirect means. This will be the case whether an investor chooses to be an indirect holder of a security or has no choice because we are issuing the securities only in global form.

For example, once we make a payment or give a notice to the legal holder, we have no further responsibility for the payment or notice even if that legal holder is required, under agreements with its participants or customers or by law, to pass it along to the indirect holders but does not do so. Similarly, we may want to obtain the approval of the holders to amend an indenture, to relieve us of the consequences of a default or of our obligation to comply with a particular provision of an indenture, or for other purposes. In such an event, we would seek approval only from the legal holders, and not the indirect holders, of the securities. Whether and how the legal holders contact the indirect holders is up to the legal holders.

21<br>

------

#### **TABLE OF CONTENTS**

#### Special Considerations for Indirect Holders
If you hold securities through a bank, broker or other financial institution, either in book-entry form because the securities are represented by one or more global securities or in street name, you should check with your own institution to find out:

&nbsp;&nbsp;&nbsp;&nbsp;• how it handles securities payments and notices;

&nbsp;&nbsp;&nbsp;&nbsp;• whether it imposes fees or charges;

&nbsp;&nbsp;&nbsp;&nbsp;• how it would handle a request for the holders' consent, if ever required;

&nbsp;&nbsp;&nbsp;&nbsp;• whether and how you can instruct it to send you securities registered in your own name so you can be a holder, if that is permitted in the future;

&nbsp;&nbsp;&nbsp;&nbsp;• how it would exercise rights under the securities if there were a default or other event triggering the need for holders to act to protect their interests; and

&nbsp;&nbsp;&nbsp;&nbsp;• if the securities are in book-entry form, how the depositary's rules and procedures will affect these matters.

#### Global Securities
A global security is a security that represents one or any other number of individual securities held by a depositary. Generally, all securities represented by the same global securities will have the same terms.

Each security issued in book-entry form will be represented by a global security that we issue to, deposit with and register in the name of a financial institution or its nominee that we select. The financial institution that we select for this purpose is called the depositary. Unless we specify otherwise in the applicable prospectus supplement, DTC will be the depositary for all securities issued in book-entry form.

A global security may not be transferred to or registered in the name of anyone other than the depositary, its nominee or a successor depositary, unless special termination situations arise. We describe those situations below under "—Special Situations When a Global Security Will Be Terminated." As a result of these arrangements, the depositary, or its nominee, will be the sole registered owner and legal holder of all securities represented by a global security, and investors will be permitted to own only beneficial interests in a global security. Beneficial interests must be held by means of an account with a broker, bank or other financial institution that in turn has an account with the depositary or with another institution that does. Thus, an investor whose security is represented by a global security will not be a legal holder of the security, but only an indirect holder of a beneficial interest in the global security.

If the prospectus supplement for a particular security indicates that the security will be issued as a global security, then the security will be represented by a global security at all times unless and until the global security is terminated. If termination occurs, we may issue the securities through another book-entry clearing system or decide that the securities may no longer be held through any book-entry clearing system.

#### Special Considerations for Global Securities
As an indirect holder, an investor's rights relating to a global security will be governed by the account rules of the investor's financial institution and of the depositary, as well as general laws relating to securities transfers. We do not recognize an indirect holder as a holder of securities and instead deal only with the depositary that holds the global security.

If securities are issued only as global securities, an investor should be aware of the following:

&nbsp;&nbsp;&nbsp;&nbsp;• an investor cannot cause the securities to be registered in his or her name, and cannot obtain non-global certificates for his or her interest in the securities, except in the special situations we describe below;

&nbsp;&nbsp;&nbsp;&nbsp;• an investor will be an indirect holder and must look to his or her own bank or broker for payments on the securities and protection of his or her legal rights relating to the securities, as we describe above;

&nbsp;&nbsp;&nbsp;&nbsp;• an investor may not be able to sell interests in the securities to some insurance companies and to other institutions that are required by law to own their securities in non-book-entry form;

&nbsp;&nbsp;&nbsp;&nbsp;• an investor may not be able to pledge his or her interest in the global security in circumstances where certificates representing the securities must be delivered to the lender or other beneficiary of the pledge in order for the pledge to be effective;

22<br>

------

#### **TABLE OF CONTENTS**
&nbsp;&nbsp;&nbsp;&nbsp;• the depositary's policies, which may change from time to time, will govern payments, transfers, exchanges and other matters relating to an investor's interest in the global security;

&nbsp;&nbsp;&nbsp;&nbsp;• we and any applicable trustee have no responsibility for any aspect of the depositary's actions or for its records of ownership interests in the global security, nor will we or any applicable trustee supervise the depositary in any way;

&nbsp;&nbsp;&nbsp;&nbsp;• the depositary may, and we understand that DTC will, require that those who purchase and sell interests in the global security within its book-entry system use immediately available funds, and your broker or bank may require you to do so as well; and

&nbsp;&nbsp;&nbsp;&nbsp;• financial institutions that participate in the depositary's book-entry system, and through which an investor holds its interest in the global security, may also have their own policies affecting payments, notices and other matters relating to the securities.

There may be more than one financial intermediary in the chain of ownership for an investor. We do not monitor and are not responsible for the actions of any of those intermediaries.

#### Special Situations When a Global Security Will Be Terminated
In a few special situations described below, a global security will terminate and interests in it will be exchanged for physical certificates representing those interests. After that exchange, the choice of whether to hold securities directly or in street name will be up to the investor. Investors must consult their own banks or brokers to find out how to have their interests in securities transferred to their own names, so that they will be direct holders. We have described the rights of holders and street name investors above.

Unless we provide otherwise in the applicable prospectus supplement, the global security will terminate when the following special situations occur:

&nbsp;&nbsp;&nbsp;&nbsp;• if the depositary notifies us that it is unwilling, unable or no longer qualified to continue as depositary for that global security and we do not appoint another institution to act as depositary within 90 days;

&nbsp;&nbsp;&nbsp;&nbsp;• if we notify any applicable trustee that we wish to terminate that global security; or

&nbsp;&nbsp;&nbsp;&nbsp;• if an event of default has occurred with regard to securities represented by that global security and has not been cured or waived.

The applicable prospectus supplement may also list additional situations for terminating a global security that would apply only to the particular series of securities covered by the applicable prospectus supplement. When a global security terminates, the depositary, and neither we nor any applicable trustee, is responsible for deciding the names of the institutions that will be the initial direct holders.

23<br>

------

#### **TABLE OF CONTENTS**

#### PLAN OF DISTRIBUTION
We may sell the securities covered hereby from time to time pursuant to underwritten public offerings, direct sales to the public, negotiated transactions, block trades or a combination of these methods. A distribution of these securities offered by this prospectus may also be effected through the issuance of derivative securities, including without limitation and warrants. We may sell the securities to or through underwriters or dealers, through agents, or directly to one or more purchasers. We may distribute securities from time to time in one or more transactions:

&nbsp;&nbsp;&nbsp;&nbsp;• at a fixed price or prices, which may be changed;

&nbsp;&nbsp;&nbsp;&nbsp;• at market prices prevailing at the time of sale;

&nbsp;&nbsp;&nbsp;&nbsp;• at prices related to such prevailing market prices; or

&nbsp;&nbsp;&nbsp;&nbsp;• at negotiated prices.

We may also sell equity securities covered by this registration statement in an "at the market offering" as defined in Rule 415 under the Securities Act. Such offering may be made into an existing trading market for such securities in transactions at other than a fixed price, either:

&nbsp;&nbsp;&nbsp;&nbsp;• on or through the facilities of the Nasdaq Capital Market or any other securities exchange or quotation or trading service on which such securities may be listed, quoted or traded at the time of sale; and/or

&nbsp;&nbsp;&nbsp;&nbsp;• to or through a market maker other than on the Nasdaq Capital Market or such other securities exchanges or quotation or trading services.

Such "at-the-market offerings," if any, may be conducted by underwriters acting as principal or agent.

A prospectus supplement or supplements (and any related free writing prospectus that we may authorize to be provided to you) will describe the terms of the offering of the securities, including, to the extent applicable:

&nbsp;&nbsp;&nbsp;&nbsp;• the name or names of any underwriters, dealers or agents, if any;

&nbsp;&nbsp;&nbsp;&nbsp;• the purchase price of the securities and the proceeds we will receive from the sale;

&nbsp;&nbsp;&nbsp;&nbsp;• any options pursuant to which underwriters may purchase additional securities from us;

&nbsp;&nbsp;&nbsp;&nbsp;• any agency fees or underwriting discounts and other items constituting agents' or underwriters' compensation;

&nbsp;&nbsp;&nbsp;&nbsp;• any public offering price;

&nbsp;&nbsp;&nbsp;&nbsp;• any discounts or concessions allowed or reallowed or paid to dealers; and

&nbsp;&nbsp;&nbsp;&nbsp;• any securities exchange or market on which the securities may be listed.

Only underwriters named in the prospectus supplement will be underwriters of the securities offered by the prospectus supplement.

If underwriters are used in the sale, they will acquire the securities for their own account and may resell the securities from time to time in one or more transactions at a fixed public offering price or at varying prices determined at the time of sale. The obligations of the underwriters to purchase the securities will be subject to the conditions set forth in the applicable underwriting agreement. We may offer the securities to the public through underwriting syndicates represented by managing underwriters or by underwriters without a syndicate. Subject to certain conditions, the underwriters will be obligated to purchase all of the securities offered by the prospectus supplement, other than securities covered by any option to purchase additional securities. Any public offering price and any discounts or concessions allowed or reallowed or paid to dealers may change from time to time. We may use underwriters with whom we have a material relationship. We will describe in the prospectus supplement, naming the underwriter, the nature of any such relationship.

We may sell securities directly or through agents we designate from time to time. We will name any agent involved in the offering and sale of securities, and we will describe any commissions and other compensation we will pay the agent in the prospectus supplement. Unless the prospectus supplement states otherwise, our agent will act on a best-efforts basis for the period of its appointment.

24<br>

------

#### **TABLE OF CONTENTS**
We may authorize agents or underwriters to solicit offers by certain types of institutional investors to purchase securities from us at the public offering price set forth in the prospectus supplement pursuant to delayed delivery contracts providing for payment and delivery on a specified date in the future. We will describe the conditions to these contracts and the commissions we must pay for solicitation of these contracts in the prospectus supplement.

We may provide agents and underwriters with indemnification against civil liabilities related to this offering, including liabilities under the Securities Act, or contribution with respect to payments that the agents or underwriters may make with respect to these liabilities. Agents and underwriters may engage in transactions with, or perform services for, us in the ordinary course of business.

All securities we may offer, other than common stock, will be new issues of securities with no established trading market. Any agents or underwriters may make a market in these securities, but will not be obligated to do so and may discontinue any market making at any time without notice. We cannot guarantee the liquidity of the trading markets for any securities. There is currently no market for any of the offered securities, other than our common stock which is listed on the Nasdaq Capital Market. We have no current plans for listing of the debt securities, preferred stock or warrants on any securities exchange or quotation system; any such listing with respect to any particular debt securities, preferred stock or warrants will be described in the applicable prospectus supplement or other offering materials, as the case may be.

Any underwriter may engage in overallotment, stabilizing transactions, short covering transactions and penalty bids in accordance with Rule 103 of Regulation M under the Exchange Act. Overallotment involves sales in excess of the offering size, which create a short position. Stabilizing transactions permit bids to purchase the underlying security so long as the stabilizing bids do not exceed a specified maximum. Short covering transactions involve purchases of the securities in the open market after the distribution is completed to cover short positions. Penalty bids permit the underwriters to reclaim a selling concession from a dealer when the securities originally sold by the dealer are purchased in a stabilizing or covering transaction to cover short positions. Those activities may cause the price of the securities to be higher than it would otherwise be. If commenced, the underwriters may discontinue any of the activities at any time. These transactions may be effected on any exchange or over-the-counter market or otherwise.

Any agents and underwriters who are qualified market makers on the Nasdaq Capital Market may engage in passive market making transactions in the securities on the Nasdaq Capital Market in accordance with Rule 103 of Regulation M, during the business day prior to the pricing of the offering, before the commencement of offers or sales of the securities. Passive market makers must comply with applicable volume and price limitations and must be identified as passive market makers. In general, a passive market maker must display its bid at a price not in excess of the highest independent bid for such security; if all independent bids are lowered below the passive market maker's bid, however, the passive market maker's bid must then be lowered when certain purchase limits are exceeded. Passive market making may stabilize the market price of the securities at a level above that which might otherwise prevail in the open market and, if commenced, may be discontinued at any time.

In compliance with guidelines of the Financial Industry Regulatory Authority, or FINRA, the maximum consideration or discount to be received by any FINRA member or independent broker dealer may not exceed 8% of the aggregate amount of the securities offered pursuant to this prospectus and any applicable prospectus supplement.

The specific terms of any lock-up provisions in respect of any given offering will be described in the applicable prospectus supplement.

25<br>

------

#### LEGAL MATTERS
Unless otherwise indicated in the applicable prospectus supplement, the validity of the securities offered by this prospectus, and any prospectus supplement thereto, will be passed upon by Cooley LLP. Additional legal matters may be passed upon for us or any underwriters, dealers or agents, by counsel that we will name in the applicable prospectus supplement.

#### EXPERTS
The consolidated financial statements as of December 31, 2021 and 2020 and for the years then ended and management's assessment of the effectiveness of internal control over financial reporting as of December 31, 2021 incorporated in this prospectus and in the registration statement of which this prospectus forms a part have been so incorporated in reliance on the reports of BDO USA, LLP, an independent registered public accounting firm, incorporated herein by reference, given on the authority of said firm as experts in auditing and accounting.

#### WHERE YOU CAN FIND MORE INFORMATION
This prospectus is part of a registration statement on Form S-3 that we filed with the SEC under the Securities Act and does not contain all the information set forth or incorporated by reference in the registration statement. Whenever a reference is made in this prospectus to any of our contracts, agreements or other documents, the reference may not be complete and you should refer to the exhibits that are a part of the registration statement or the exhibits to the reports or other documents incorporated by reference into this prospectus for a copy of such contract, agreement or other document.

We file annual, quarterly and current reports, proxy statements and other information with the SEC. Our SEC filings are available to the public over the Internet at the SEC's website at http://www.sec.gov. Our Annual Report on Form 10-K, Quarterly Reports on Form 10-Q and Current Reports on Form 8-K, including any amendments to those reports, and other information that we file with or furnish to the SEC pursuant to Section 13(a) or 15(d) of the Exchange Act can also be accessed free of charge on the Investor section of our website. These filings will be available as soon as reasonably practicable after we electronically file such material with, or furnish it to, the SEC.

Our website address is www.bionanogenomics.com. Information contained on or accessible through our website is not a part of this prospectus and is not incorporated by reference herein, and the inclusion of our website address in this prospectus is an inactive textual reference only.

26<br>

------

#### **TABLE OF CONTENTS**

#### INCORPORATION OF CERTAIN INFORMATION BY REFERENCE
The SEC allows us to "incorporate by reference" information into this prospectus, which means that we can disclose important information to you by referring you to another document filed separately with the SEC. The SEC file number for the documents incorporated by reference in this prospectus is 001-38613. The documents incorporated by reference into this prospectus contain important information that you should read about us.

The following documents are incorporated by reference into this document:

&nbsp;&nbsp;&nbsp;&nbsp;• our Annual Report on Form 10-K for the year ended December 31, 2021, filed with the SEC on [March 1, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000007/bngo-20211231.htm) ;

&nbsp;&nbsp;&nbsp;&nbsp;• our Quarterly Reports on Form 10-Q for the quarters ended March 31, 2022, June 30, 2022 and September 30, 2022 filed with the SEC on [May 5, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000013/bngo-20220331.htm) , [August 4, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000021/bngo-20220630.htm) and [November 3, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000029/bngo-20220930.htm) , respectively;

&nbsp;&nbsp;&nbsp;&nbsp;• certain portions of our Definitive Proxy Statement on Schedule 14A specifically incorporated by reference into our Annual Report on Form 10-K for the year ended December 31, 2021 (other than information furnished rather than filed), filed with the SEC on [April 27, 2022](https://www.sec.gov/Archives/edgar/data/1411690/000114036122016251/ny20002836x1_def14a.htm) ;

&nbsp;&nbsp;&nbsp;&nbsp;• our Current Reports on Form 8-K (other than information furnished rather than filed) filed with the SEC on [February 23, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122006392/brhc10034332_8k.htm) , [June 10, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122022621/brhc10038653_8k.htm) , [November 18, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/0001411690/000114036122042327/brhc10044406_8k.htm) , [November 28, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/0001411690/000114036122043313/brhc10044740_form8k.htm) , [November 29, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/0001411690/000114036122043393/brhc10044743_8k.htm) , [November 30, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/0001411690/000114036122043729/brhc10044882_8k.htm) , and [February 3, 2023](https://www.sec.gov/ix?doc=/Archives/edgar/data/0001411690/000114036123004345/brhc10047533_8k.htm) to the extent the information in such reports is filed and not furnished; and

&nbsp;&nbsp;&nbsp;&nbsp;• the description of our common stock in our registration statement on Form 8-A, which was filed with the SEC on [August 17, 2018](https://www.sec.gov/Archives/edgar/data/1411690/000119312518251675/d610675d8a12ba.htm) , including all amendments and reports filed for the purpose of updating such description, including Exhibit 4.12 Annual Report on Form 10-K for the year ended December 31, 2021.

We also incorporate by reference into this prospectus all documents (other than current reports furnished under Item 2.02 or Item 7.01 of Form 8-K and exhibits filed on such form that are related to such items) that are filed by us with the SEC pursuant to Sections 13(a), 13(c), 14 or 15(d) of the Exchange Act (i) after the date of the initial filing of the registration statement of which this prospectus forms a part and prior to effectiveness of the registration statement, and (ii) after the effectiveness of the registration statement but prior to the termination of all offerings of securities covered by this prospectus. These documents include periodic reports, such as Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q and Current Reports on Form 8-K, as well as proxy statements. Any statement contained herein or in a document incorporated or deemed to be incorporated by reference into this document will be deemed to be modified or superseded for purposes of the document to the extent that a statement contained in this document or any other subsequently filed document that is deemed to be incorporated by reference into this document modifies or supersedes the statement.

We will provide to each person, including any beneficial owner, to whom a prospectus is delivered, without charge upon written or oral request, a copy of any or all of the documents that are incorporated by reference into this prospectus but not delivered with the prospectus, including exhibits which are specifically incorporated by reference into such documents. You should direct any requests for documents by writing us at Bionano Genomics, Inc., 9540 Towne Centre Drive, Suite 100, San Diego, California 92121 or telephoning us at (858) 888-7600.

27<br>

------

#### **TABLE OF CONTENTS**

#### PROSPECTUS SUPPLEMENT<br>

#### (to Prospectus dated March 9, 2023)

#### $200,000,000
![](logo_bionanox1.jpg)<br>

#### Common Stock
We previously entered into a sales agreement, or the sales agreement, with Cowen and Company, LLC, or TD Cowen, relating to shares of our common stock, par value $0.0001 per share, offered by this prospectus supplement. In accordance with the terms of the sales agreement, we may offer and sell shares of our common stock from time to time through TD Cowen, acting as sales agent. We originally filed a prospectus supplement, dated March 24, 2021, or the Prior Prospectus Supplement, for the offer and sale of up to $350,000,000 of shares of our common stock, from time to time through TD Cowen, acting as our agent, pursuant to the sales agreement under the shelf registration statement on Form S-3 (Registration Statement No. 333-252216). As of the date of this prospectus supplement, we have issued and sold approximately $52,233,273 of our common stock pursuant to the sales agreement and the Prior Prospectus Supplement. The common stock remaining available to be sold under the Prior Prospectus Supplement as of the date of this prospectus supplement will no longer be offered and sold under the Prior Prospectus Supplement, but will instead be offered and sold under this prospectus supplement, subject to a reduction of the maximum aggregate amount for which we can offer and sell shares of our common stock pursuant to the sales agreement to $200,000,000. Accordingly, we may offer and sell shares of our common stock having an aggregate offering price of up to $200,000,000.

Our common stock is listed on the Nasdaq Capital Market under the symbol "BNGO." On March 8, 2023, the last reported sale price of our common stock was $1.31 per share.

Sales of our common stock, if any, under this prospectus supplement and the accompanying prospectus will be made in sales deemed to be "at the market offerings" as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended, or the Securities Act. TD Cowen is not required to sell any specific amount of securities, but will act as our sales agent using commercially reasonable efforts consistent with its normal trading and sales practices, on mutually agreed terms between TD Cowen and us. There is no arrangement for funds to be received in any escrow, trust or similar arrangement. Under the sales agreement, we may also sell shares of common stock to TD Cowen as principal for its own account, at a price to be agreed upon at the time of sale. If we sell shares to a TD Cowen as principal, we will enter into a separate terms agreement with TD Cowen, and we will describe the agreement in a separate prospectus supplement or pricing supplement.

The compensation to TD Cowen for sales of common stock sold pursuant to the sales agreement will be an amount up to 3.0% of the gross proceeds of any shares of common stock sold under the sales agreement. In connection with the sale of the common stock on our behalf, TD Cowen will be deemed to be an "underwriter" within the meaning of the Securities Act and the compensation of TD Cowen will be deemed to be underwriting commissions or discounts. We have also agreed to provide indemnification and contribution to TD Cowen with respect to certain liabilities, including liabilities under the Securities Act or the Securities Exchange Act of 1934, as amended, or the Exchange Act.

As of December 31, 2022, we had 63,218,433 authorized but unissued shares of our common stock available for issuance (after deducting the number of shares of our common stock issuable upon exercise, conversion or exchange of our outstanding securities or otherwise reserved for future issuance). Based on such number of available authorized but unissued shares of our common stock and an assumed offering price per share of $1.31, which was the last reported sale price of our common stock on Nasdaq on March 8, 2023, we would be able to issue and sell up to $82,816,147 of shares under our sales agreement, notwithstanding the $200,000,000 maximum aggregate offering amount set forth in this prospectus supplement. In no event will we sell, pursuant to the registration statement of which this prospectus supplement forms a part, more shares of our common stock than we have available and authorized for issuance.

**Our business and an investment in our common stock involve significant risks. These risks are described under the caption "Risk Factors" beginning on page S-[4](#pRF1) of this prospectus supplement, page [6](#tRF) of the accompanying prospectus, as well as those risks described in our most recent Annual Report on Form 10-K and in our other filings with the Securities and Exchange Commission that are incorporated by reference into this prospectus supplement.** 

**Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus supplement is truthful or complete. Any representation to the contrary is a criminal offense.**

### TD COWEN

#### The date of this prospectus supplement is March 9, 2023.

------

#### **TABLE OF CONTENTS**

#### Prospectus Supplement

---

| | |
|:---|:---|
| [ABOUT THIS PROSPECTUS SUPPLEMENT](#pAT1) | [S-ii](#pAT1) |
| [PROSPECTUS SUPPLEMENT SUMMARY](#pPS1) | &nbsp;&nbsp;[S-1](#pPS1) |
| [THE OFFERING](#pTO1) | &nbsp;&nbsp;[S-2](#pTO1) |
| [RISK FACTORS](#pRF1) | &nbsp;&nbsp;[S-4](#pRF1) |
| [SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS](#pSN1) | &nbsp;&nbsp;[S-6](#pSN1) |
| [USE OF PROCEEDS](#pUO1) | &nbsp;&nbsp;[S-8](#pUO1) |
| [DILUTION](#pDI1) | &nbsp;&nbsp;[S-9](#pDI1) |
| [PLAN OF DISTRIBUTION](#pPO1) | [S-11](#pPO1) |
| [LEGAL MATTERS](#pLM1) | [S-12](#pLM1) |
| [EXPERTS](#pEX1) | [S-12](#pEX1) |
| [WHERE YOU CAN FIND ADDITIONAL INFORMATION](#pWYC1) | [S-12](#pWYC1) |
| [INCORPORATION OF CERTAIN INFORMATION BY REFERENCE](#pIOC1) | [S-13](#pIOC1) |

---

S-i<br>

------

#### **TABLE OF CONTENTS**

#### ABOUT THIS PROSPECTUS SUPPLEMENT
This prospectus supplement and the accompanying prospectus relate to the offering of our common stock. Before buying any of the common stock that we are offering, we urge you to carefully read this prospectus supplement, together with the information incorporated by reference in this prospectus supplement, and any free writing prospectus supplement or prospectus supplement that we have authorized for use in connection with this offering when making your investment decision. You should also read and consider the information in the documents we have referred you to under the headings "Where You Can Find More Information" and "Incorporation of Certain Information by Reference." These documents contain important information that you should consider when making your investment decision.

This document is in two parts. The first part is this prospectus supplement, which describes the specific terms of the common stock we are offering and also adds to and updates information contained in the accompanying prospectus and the documents incorporated by reference herein or therein. The second part, the accompanying prospectus, including the documents incorporated by reference therein, provides more general information. Generally, when we refer to this prospectus, we are referring to both parts of this document combined. To the extent there is a conflict between the information contained in this prospectus supplement and the information contained in the accompanying prospectus or any document incorporated by reference herein or therein filed prior to the date of this prospectus supplement, you should rely on the information in this prospectus supplement; provided that if any statement in one of these documents is inconsistent with a statement in another document having a later date—for example, a document incorporated by reference in the accompanying prospectus—the statement in the document having the later date modifies or supersedes the earlier statement.

You should rely only on the information contained in or incorporated by reference in this prospectus supplement, in the accompanying prospectus and any free writing prospectus or prospectus supplement that we have authorized for use in connection with this offering. We have not, and the sales agent has not, authorized anyone to provide you with different information. If anyone provides you with different or inconsistent information, you should not rely on it. We are not, and the sales agent is not, making an offer to sell these securities in any jurisdiction where the offer or sale is not permitted.

You should assume that the information appearing in this prospectus supplement, the documents incorporated by reference in this prospectus supplement, in the accompanying prospectus and any free writing prospectus or prospectus supplement that we have authorized for use in connection with this offering, is accurate only as of the date of those respective documents. Our business, financial condition, results of operations and prospects may have changed since those dates. You should read this prospectus supplement, the accompanying prospectus, the documents incorporated by reference in this prospectus supplement and in the accompanying prospectus, and any free writing prospectus or prospectus supplement that we have authorized for use in connection with this offering, in their entirety before making an investment decision.

Unless otherwise mentioned or unless the context requires otherwise, all references in this prospectus supplement and the accompanying prospectus to "Bionano," "we," "us" and "our" refer to Bionano Genomics, Inc. and its subsidiaries or, as the context may require, Bionano Genomics, Inc. only. "Bionano Laboratories," "BioDiscovery" and "Purigen" refer to our wholly owned subsidiaries, Lineagen, Inc. (doing business as Bionano Laboratories), BioDiscovery, LLC and Purigen Biosystems, Inc., respectively.

This prospectus supplement, the accompanying prospectus and the information incorporated by reference herein or therein include trademarks, service marks and trade names owned by us or other companies. All trademarks, service marks and trade names included or incorporated by reference into this prospectus supplement and the accompanying prospectus are the property of their respective owners.

S-ii<br>

------

#### **TABLE OF CONTENTS**

#### PROSPECTUS SUPPLEMENT SUMMARY
*The following summary highlights certain information about us, this offering and selected information contained elsewhere in or incorporated by reference into this prospectus supplement. This summary is not complete and does not contain all of the information that you should consider before deciding whether to invest in our securities. For a more complete understanding of our company and this offering, you should read and consider carefully the more detailed information included or incorporated by reference in this prospectus supplement and the accompanying prospectus, including the factors described under the heading "Risk Factors," as well as the information included in any free writing prospectus that we have authorized for use in connection with this offering.*

#### Company Overview
We are a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. Our mission is to transform the way the world sees the genome through optical genome mapping, or OGM, solutions, diagnostic services and software. We offer OGM solutions, including our Saphyr system, for applications across basic, translational and clinical research, and for other applications including cell bioprocessing quality control. Through our Bionano Laboratories business, we also provide diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through our BioDiscovery business, we offer an industry-leading, platform-agnostic software solution, our NxClinical software, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. Through our Purigen business, we offer nucleic acid extraction and purification solutions using proprietary isotachophoresis technology, through our Ionic Purification system.

#### Corporate Information
We were formed in January 2003 as BioNanomatrix LLC, a Delaware limited liability company. In August 2007, we became BioNanomatrix Inc., a Delaware corporation. In October 2011, we changed our name to BioNano Genomics, Inc., and in July 2018, we changed our name to Bionano Genomics, Inc.

Our principal executive offices are located at 9540 Towne Centre Drive, Suite 100, San Diego, California 92121, and our telephone number is (858) 888-7600. Our website address is www.bionanogenomics.com and we regularly post copies of our press releases as well as additional information about us on our website. Information contained in, or that can be accessed through, our website is not incorporated by reference into this prospectus supplement and the accompanying prospectus, and you should not consider information on our website to be part of this prospectus or in deciding whether to purchase our securities.

Our design logo, "Bionano," and our other registered and common law trade names, trademarks and service marks are the property of Bionano Genomics, Inc. The trademarks, trade names and service marks appearing in this prospectus supplement and the accompanying prospectus are the property of their respective owners. We do not intend our use or display of other companies' trademarks, trade names or service marks to imply a relationship with, or endorsement or sponsorship of us by, any other companies or products.

#### Implications of Being a Smaller Reporting Company
We are a "smaller reporting company" and accordingly may provide less public disclosure than larger public companies, including the inclusion of only two years of audited financial statements and only two years of related selected financial data and management's discussion and analysis of financial condition and results of operations disclosure. As a result, the information that we provide to our stockholders may be different than you might receive from other public reporting companies in which you hold equity interests.

S-1<br>

------

#### **TABLE OF CONTENTS**

#### THE OFFERING

#### Common stock offered by us
Shares of our common stock having an aggregate offering price of up to $200,000,000.

#### Common stock to be outstanding immediately following this offering
449,854,559 shares, assuming sales of 152,671,755 shares in this offering at an assumed offering price of $1.31 per share, which was the last reported sale price of our common stock on the Nasdaq Capital Market on March 8, 2023. The actual number of shares issued will vary depending on how many shares of our common stock we choose to sell and the prices at which such sales occur, and in no event will the actual number of shares issued and sold pursuant to the sales agreement exceed the number of shares of our common stock that we have available and authorized for issuance under our certificate of incorporation, as the same may be amended or amended and restated from time to time.

#### Plan of Distribution
"At-the-market" offering that may be made from time to time through our sales agent, Cowen and Company, LLC. See "Plan of Distribution" on page S-[11](#pPO1) of this prospectus supplement.

#### Use of Proceeds
We intend to use the net proceeds from the offering to support our growth strategy and for working capital and general corporate purposes, including research and development expenses, discharge of indebtedness and capital expenditures. See "Use of Proceeds."

#### Risk Factors
Investing in our securities involves a high degree of risk. See "Risk Factors" on page S-[4](#pRF1) of this prospectus supplement and under similar headings in other documents incorporated by reference herein.

#### Nasdaq Capital Market Symbol
BNGO

The number of shares of our common stock to be outstanding immediately after this offering as shown above is based on 297,182,804 shares of our common stock outstanding as of December 31, 2022, and excludes:

&nbsp;&nbsp;&nbsp;&nbsp;• 24,022,000 shares of common stock issuable upon the exercise of options outstanding as of December 31, 2022 at a weighted average exercise price of $3.28 per share;

&nbsp;&nbsp;&nbsp;&nbsp;• 8,637,038 shares of common stock reserved for future issuance under our 2018 Equity Incentive Plan, or the 2018 Plan, as of December 31, 2022, plus any future increases in the number of shares of common stock reserved for issuance under the 2018 Plan pursuant to evergreen provisions;

&nbsp;&nbsp;&nbsp;&nbsp;• 137,723 shares of common stock reserved for future issuance under our 2018 Employee Stock Purchase Plan, or the 2018 ESPP, as of December 31, 2022, plus any future increases in the number of shares of common stock reserved for issuance under the 2018 ESPP pursuant to evergreen provisions;

&nbsp;&nbsp;&nbsp;&nbsp;• 2,060,002 shares of common stock reserved for future issuance under our 2020 Inducement Plan as of December 31, 2022;

&nbsp;&nbsp;&nbsp;&nbsp;• 96,000 shares of common stock issuable upon the vesting and settlement of restricted stock units outstanding as of December 31, 2022;

&nbsp;&nbsp;&nbsp;&nbsp;• 290,000 shares of common stock issuable upon the vesting and settlement of performance-based restricted stock units outstanding as of December 31, 2022; and

&nbsp;&nbsp;&nbsp;&nbsp;• 4,356,000 shares of common stock issuable upon the exercise of common warrants outstanding as of December 31, 2022 at a weighted-average exercise price of $5.96 per share, under which no shares of common stock have been issued between January 1, 2023 and February 28, 2023.

S-2<br>

------

#### **TABLE OF CONTENTS**
Except as otherwise indicated, the information in this prospectus supplement assumes no exercise of the outstanding stock options or common warrants summarized above and no vesting or settlement of the outstanding restricted stock units summarized above.

In addition, the number of shares of our common stock to be outstanding immediately after this offering as shown above does not include 8,339,843 shares of our common stock issued between January 1, 2023 and February 28, 2023 pursuant to the sales agreement.

S-3<br>

------

#### RISK FACTORS
*An investment in our securities involves a high degree of risk. You should carefully consider the following risk factors and the risk factors discussed under the section entitled "Risk Factors" contained in our Annual Report on Form 10-K for the year ended December 31, 2021, as updated by our subsequent filings, which are incorporated by reference into this prospectus supplement and accompanying prospectus in their entirety, together with all of the other information contained in this prospectus supplement and the accompanying prospectus or incorporated by reference into this prospectus supplement and the accompanying prospectus. The risks and uncertainties described in these documents are not the only ones we face. Other risks and uncertainties, including those that we do not currently consider material, may impair our business. If any of the risks discussed below or incorporated by reference actually occur, our business, financial condition, operating results or cash flows could be materially adversely affected. This could cause the value of our securities to decline, and you may lose all or part of your investment.*

#### Risks Related to this Offering

#### Management will have broad discretion as to the use of the proceeds from this offering, and we may not use the proceeds effectively.
Our management will have broad discretion in the application of the net proceeds we receive from this offering, including for any of the purposes described in the section entitled "Use of Proceeds," and you will not have the opportunity as part of your investment decision to assess whether the net proceeds are being used appropriately. Because of the number and variability of factors that will determine our use of the net proceeds from this offering, their ultimate use may vary substantially from their currently intended use. Our management could spend the proceeds in ways that do not improve our results of operations or enhance the value of our common stock. Our failure to apply these funds effectively could have a material adverse effect on our business, delay the development of our product candidates and cause the price of our common stock to decline.

***If you purchase the common stock sold in this offering, you will experience immediate and substantial dilution in your investment. You will experience further dilution if we issue additional equity securities in future fundraising transactions.***

Since the price per share of our common stock being offered is substantially higher than the net tangible book value per share of our common stock, you will suffer substantial dilution with respect to the net tangible book value of the common stock you purchase in this offering. Based on our net tangible book value as of December 31, 2022, if you purchase shares of common stock in this offering, you will suffer immediate and substantial dilution of $0.57 per share with respect to the net tangible book value of our common stock. See the section of this prospectus supplement entitled "Dilution" for a more detailed discussion of the dilution you will incur if you purchase common stock in this offering.

In addition, we have a significant number of stock options and warrants outstanding. To the extent that outstanding stock options or warrants have been or may be exercised or other securities issued, investors purchasing our common stock in this offering may experience further dilution. In addition, we may choose to raise additional capital due to market conditions or strategic considerations even if we believe we have sufficient funds for our current or future operating plans. To the extent that additional capital is raised through the sale of equity or convertible debt securities, the issuance of these securities could result in further dilution to our stockholders or result in downward pressure on the price of our common stock.

#### Future sales of our common stock, or the perception that such future sales may occur, may cause our stock price to decline.
Sales of a substantial number of shares of our common stock in the public market, or the perception that these sales could occur, following this offering could cause the market price of our common stock to decline. A substantial majority of the outstanding shares of our common stock are, and the shares of common stock sold in this offering upon issuance will be, freely tradable without restriction or further registration under the Securities Act.

***We do not currently intend to pay dividends on our common stock, and any return to investors is expected to come, if at all, only from potential increases in the price of our common stock.***

At the present time, we intend to use available funds to finance our operations. Accordingly, while payment of dividends rests within the discretion of our board of directors, we have no intention of paying any such dividends in the foreseeable future. Any return to investors is expected to come, if at all, only from potential increases in the price of our common stock.

S-4<br>

------

#### **TABLE OF CONTENTS**
***The actual number of shares we will issue under the sales agreement with the sales agent, at any one time or in total, is uncertain.***

Subject to certain limitations in the sales agreement with the agent and compliance with applicable law, we have the discretion to deliver placement notices to the sales agents at any time throughout the term of the sales agreement. The number of shares that are sold by the agent after delivering a placement notice will fluctuate based on the market price of the common stock during the sales period and limits we set with the agent.

***An increase in the number of authorized shares or the trading price of our common stock will be required for us to offer and sell up to the entire aggregate offering price under the sales agreement. If we are not able to increase the number of authorized shares of our common stock or our trading price does not increase, we may be limited in our ability to issue and sell our shares under the sales agreement, and, as a result, our operations and financial condition may be materially and adversely affected.***

We will need to seek the additional capital necessary to fund our operations through public or private equity offerings, debt financings, and collaborative and licensing arrangements, including through sales under the sales agreement. We have limited shares of our common stock currently available and authorized for issuance. Investors in prior transactions have purchased our shares of common stock or our convertible securities, such as warrants, for which we must reserve unissued shares of our common stock. We therefore will likely need to increase the number of authorized shares of our common stock, which requires stockholder approval, in order to issue shares of our common stock or securities convertible, exercisable or exchangeable into shares of our common stock to investors and other strategic partners, to utilize the full availability under the sales agreement or in other capital raising transactions. If our trading price does not increase or if we are unable to increase the authorized shares of our common stock, we will be limited in our efforts to raise additional capital, including through this offering. As a result, our operations and financial condition may be materially and adversely affected.

S-5<br>

------

#### SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS
This prospectus supplement and the accompanying prospectus, including the documents incorporated by reference herein and therein, and any free writing prospectus that we have authorized for use in connection with this offering, contain forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. These statements are based on our management's current beliefs, expectations and assumptions about future events, conditions and results and on information currently available to us. Discussions containing these forward-looking statements may be found, among other places, in the sections titled "Business," "Risk Factors" and "Management's Discussion and Analysis of Financial Condition and Results of Operations" incorporated by reference from our most recent Annual Report on Form 10-K and our subsequent Quarterly Reports on Form 10-Q filed with the SEC, as well as any amendments thereto reflected in subsequent filings with the SEC.

Any statements in this prospectus supplement or the accompanying prospectus, or incorporated by reference herein or therein, and any free writing prospectus, about our expectations, beliefs, plans, objectives, assumptions or future events or performance are not historical facts and are forward-looking statements. Within the meaning of Section 27A of the Securities Act and Section 21E of the Exchange Act, these forward-looking statements include statements regarding:

&nbsp;&nbsp;&nbsp;&nbsp;• the size and growth potential of the markets for our products, and our ability to serve those markets;

&nbsp;&nbsp;&nbsp;&nbsp;• the rate and degree of market acceptance of our products;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to manage the growth of our business and integrate acquired businesses;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to expand our commercial organization to address effectively existing and new markets that we intend to target;

&nbsp;&nbsp;&nbsp;&nbsp;• the impact from future regulatory, judicial, and legislative changes or developments in the U.S. and foreign countries;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to successfully execute our strategy and meet anticipated goals and milestones;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to compete effectively in a competitive industry;

&nbsp;&nbsp;&nbsp;&nbsp;• the introduction of competitive technologies or improvements in existing technologies and the success of any such technologies;

&nbsp;&nbsp;&nbsp;&nbsp;• the performance of our third-party contract sales organizations, suppliers and manufacturers;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to attract and retain key scientific or management personnel;

&nbsp;&nbsp;&nbsp;&nbsp;• the accuracy of our estimates regarding expenses, future revenues, reimbursement rates, capital requirements and needs for additional financing;

&nbsp;&nbsp;&nbsp;&nbsp;• the impact of geopolitical and macroeconomic developments, such as the ongoing conflict between Ukraine and Russia, related sanctions and the COVID-19 pandemic on our business and operations, as well as the business or operations of our suppliers, customers, manufacturers, research partners and other third parties with whom we conduct business and our expectations with respect to the duration of such impacts and the resulting effects on our business;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to realize the anticipated benefits and synergies of our recent and any future acquisitions or other strategic transactions;

&nbsp;&nbsp;&nbsp;&nbsp;• our intended use of the net proceeds from offerings of shares of our common stock under this prospectus supplement;

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to obtain funding for our operations; and

&nbsp;&nbsp;&nbsp;&nbsp;• our ability to attract collaborators and strategic partnerships.

In some cases, you can identify forward-looking statements by terminology such as "anticipate," "believe," "continue," "could," "estimate," "expects," "intend," "may," "might," "plan," "potential," "predict," "project," "should," "will," "would" or the negative or plural of those terms, and similar expressions intended to identify statements about the future, although not all forward-looking statements contain these words. These statements involve known and unknown risks, uncertainties and other factors that may cause our actual results, levels of activity,

S-6<br>

------

#### **TABLE OF CONTENTS**
performance or achievements to be materially different from the information expressed or implied by these forward-looking statements. In addition, statements that "we believe" and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this prospectus, and while we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain and investors are cautioned not to unduly rely upon these statements.

You should refer to the risks and uncertainties described in the "Risk Factors" section contained in this prospectus supplement, the accompanying prospectus and any related free writing prospectus, and under similar headings in the other documents that are incorporated by reference into this prospectus supplement and the accompanying prospectus, for a discussion of important factors that may cause our actual results to differ materially from those expressed or implied by our forward-looking statements. Given these risks, uncertainties and other factors, many of which are beyond our control, we cannot assure you that the forward-looking statements in this prospectus supplement and the accompanying prospectus will prove to be accurate, and you should not place undue reliance on these forward-looking statements. Furthermore, if our forward-looking statements prove to be inaccurate, the inaccuracy may be material. In light of the significant uncertainties in these forward-looking statements, you should not regard these statements as a representation or warranty by us or any other person that we will achieve our objectives and plans in any specified time frame, or at all.

Except as required by law, we assume no obligation to update these forward-looking statements publicly, or to revise any forward-looking statements to reflect events or developments occurring after the date of this prospectus supplement, even if new information becomes available in the future.

S-7<br>

------

#### USE OF PROCEEDS
We may issue and sell shares of our common stock having aggregate sales proceeds of up to $200,000,000 from time to time after the date of this prospectus supplement. Because there is no minimum offering amount required as a condition to close this offering, the actual total public offering amount, commissions and proceeds to us, if any, are not determinable at this time. There can be no assurance that we will sell any shares under or fully utilize the sales agreement with TD Cowen as a source of financing.

We currently intend to use the net proceeds from the sale of the common stock offered by us hereunder to support our growth strategy and for working capital and general corporate purposes, including research and development expenses and capital expenditures. We may also use a portion of the net proceeds from this offering to co-develop, acquire or invest in products, technologies or businesses that are complementary to our business. However, we currently have no agreements or commitments for any such uses of proceeds.

The amounts and timing of our use of the net proceeds from this offering will depend on a number of factors, such as the timing and progress of our research and development efforts, the timing and progress of any partnering and commercialization efforts, technological advances and the competitive environment for our products. As of the date of this prospectus supplement, we cannot specify with certainty all of the particular uses for the net proceeds to us from the sale of the securities offered by us hereunder. Accordingly, our management will have broad discretion in the timing and application of these proceeds. Pending application of the net proceeds as described above, we intend to temporarily invest the proceeds in short-term, interest-bearing instruments.

S-8<br>

------

#### **TABLE OF CONTENTS**

#### DILUTION
Our net tangible book value as of December 31, 2022 was approximately $131.0 million, or $0.44 per share of common stock. Net tangible book value per share is determined by dividing our total tangible assets (total assets, less intangible assets), less total liabilities, by the number of shares of our common stock outstanding as of December 31, 2022.

After giving effect to our sale of 152,671,755 shares of common stock, assuming all such shares are available and authorized for issuance at the time of such sale, during the term of the sales agreement with the agent in the aggregate amount of $200,000,000 at an assumed public offering price of $1.31 per share, which was the last reported sale price of our common stock on the Nasdaq Capital Market on March 8, 2022, and after deducting underwriting discounts and commissions and estimated offering expenses payable by us, our as adjusted net tangible book value as of December 31, 2022 would have been $331.0 million, or $0.74 per share of common stock. This represents an immediate increase in net tangible book value of $0.30 per share to existing stockholders and an immediate dilution in net tangible book value of $0.57 per share to purchasers of common stock in this offering. Dilution per share to new investors represents the difference between the amount per share paid by purchasers of shares of common stock in this offering and the as adjusted net tangible book value per share of common stock immediately after completion of this offering. The following table illustrates this dilution on a per share basis:

---

| | | |
|:---|:---|:---|
| Assumed public offering price per share |  | $1.31 |
| &nbsp;&nbsp;&nbsp;Net tangible book value per share as of December 31, 2022 | $0.44 |  |
| &nbsp;&nbsp;&nbsp;Increase in net tangible book value per share attributable to this offering | $0.30 |  |
| As adjusted net tangible book per share as of December 31, 2022, after giving effect to this offering |  | $0.74 |
| Dilution per share to investors in this offering |  | $0.57 |

---

The table above is based on 297,182,804 shares of our common stock outstanding as of December 31, 2022, and excludes:

&nbsp;&nbsp;&nbsp;&nbsp;• 24,022,000 shares of common stock issuable upon the exercise of options outstanding as of December 31, 2022 at a weighted average exercise price of $3.28 per share;

&nbsp;&nbsp;&nbsp;&nbsp;• 8,637,038 shares of common stock reserved for future issuance under our 2018 Plan as of December 31, 2022, plus any future increases in the number of shares of common stock reserved for issuance under the 2018 Plan pursuant to evergreen provisions;

&nbsp;&nbsp;&nbsp;&nbsp;• 137,723 shares of common stock reserved for future issuance under our 2018 ESPP as of December 31, 2022, plus any future increases in the number of shares of common stock reserved for issuance under the 2018 ESPP pursuant to evergreen provisions;

&nbsp;&nbsp;&nbsp;&nbsp;• 2,060,002 shares of common stock reserved for future issuance under our 2020 Inducement Plan as of December 31, 2022;

&nbsp;&nbsp;&nbsp;&nbsp;• 96,000 shares of common stock issuable upon the vesting and settlement of restricted stock units outstanding as of December 31, 2022;

&nbsp;&nbsp;&nbsp;&nbsp;• 290,000 shares of common stock issuable upon the vesting and settlement of performance-based restricted stock units outstanding as of December 31, 2022; and

&nbsp;&nbsp;&nbsp;&nbsp;• 4,356,000 shares of common stock issuable upon the exercise of common warrants outstanding as of December 31, 2022 at a weighted-average exercise price of $5.96 per share, under which no shares of common stock have been issued between January 1, 2023 and February 28, 2023.

To the extent that outstanding options or warrants have been or may be exercised, outstanding restricted stock units may vest and settle, or other shares issued, investors purchasing our securities in this offering may experience further dilution. In addition, we may choose to raise additional capital due to market conditions or strategic considerations even if we believe we have sufficient funds for our current or future operating plans. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the issuance of these securities could result in further dilution to our stockholders.

S-9<br>

------

#### **TABLE OF CONTENTS**
Except as otherwise indicated, the information in this prospectus supplement assumes no exercise of the outstanding stock options or common warrants summarized above and no vesting or settlement of the outstanding restricted stock units summarized above. In addition, the number of shares of our common stock to be outstanding immediately after this offering as shown above does not include 8,339,843 shares of our common stock issued between January 1, 2023 and February 28, 2023 pursuant to the sales agreement.

S-10<br>

------

#### PLAN OF DISTRIBUTION
We have entered into a sales agreement with TD Cowen, under which we may issue and sell from time to time up to $200,000,000 of our common stock through or to TD Cowen as our sales agent or principal. In no event will we sell, pursuant to the registration statement of which this prospectus supplement forms a part, more shares of our common stock than we have available and authorized for issuance. Sales of our common stock, if any, will be made at market prices by any method that is deemed to be an "at the market offering" as defined in Rule 415(a)(4) under the Securities Act.

TD Cowen will offer our common stock subject to the terms and conditions of the sales agreement on a daily basis or as otherwise agreed upon by us and TD Cowen. We will designate the maximum amount of common stock to be sold through TD Cowen on a daily basis or otherwise determine such maximum amount together with TD Cowen. Subject to the terms and conditions of the sales agreement, TD Cowen will use its commercially reasonable efforts to sell on our behalf all of the shares of common stock requested to be sold by us. We may instruct TD Cowen not to sell common stock if the sales cannot be effected at or above the price designated by us in any such instruction. TD Cowen or we may suspend the offering of our common stock being made through TD Cowen under the sales agreement upon proper notice to the other party. TD Cowen and we each have the right, by giving written notice as specified in the sales agreement, to terminate the sales agreement in each party's sole discretion at any time.

The aggregate compensation payable to TD Cowen as sales agent up to 3.0% of the gross sales price of the shares sold through it pursuant to the sales agreement. We have also agreed to reimburse TD Cowen up to $50,000 of TD Cowen's actual outside legal expenses incurred by TD Cowen in connection with this offering, d for certain other expenses, including Cowen's FINRA counsel fees in an amount up to $10,000. We estimate that the total expenses of the offering payable by us, excluding commissions payable to TD Cowen under the sales agreement, will be approximately $300,000.

The remaining sales proceeds, after deducting any expenses payable by us and any transaction fees imposed by any governmental, regulatory, or self-regulatory organization in connection with the sales, will equal our net proceeds for the sale of such common stock.

TD Cowen will provide written confirmation to us following the close of trading on The Nasdaq Capital Market on each day in which common stock is sold through it as sales agent under the sales agreement. Each confirmation will include the number of shares of common stock sold through it as sales agent on that day, the volume weighted average price of the shares sold, the percentage of the daily trading volume and the net proceeds to us.

We will report at least quarterly the number of shares of common stock sold through TD Cowen under the sales agreement, the net proceeds to us and the compensation paid by us to TD Cowen in connection with the sales of common stock.

Settlement for sales of common stock will occur, unless the parties agree otherwise, on the second business day that is also a trading day following the date on which any sales were made in return for payment of the net proceeds to us. There is no arrangement for funds to be received in an escrow, trust or similar arrangement.

Under the sales agreement, we may also sell shares of common stock to TD Cowen as principal for its own account, at a price to be agreed upon at the time of sale. If we sell shares to a TD Cowen as principal, we will enter into a separate terms agreement with TD Cowen, and we will describe the agreement in a separate prospectus supplement or pricing supplement.

In connection with the sales of our common stock on our behalf, TD Cowen will be deemed to be an "underwriter" within the meaning of the Securities Act, and the compensation paid to TD Cowen will be deemed to be underwriting commissions or discounts. We have agreed in the sales agreement to provide indemnification and contribution to TD Cowen against certain liabilities, including liabilities under the Securities Act. As sales agent, TD Cowen will not engage in any transactions that stabilizes our common stock.

Our common stock is listed on the Nasdaq Capital Market and trades under the symbol "BNGO." The transfer agent of our common stock is American Stock Transfer & Trust Company, LLC.

TD Cowen and/or its affiliates have provided, and may in the future provide, various investment banking and other financial services for us for which services they have received and, may in the future receive, customary fees.

S-11<br>

------

#### **TABLE OF CONTENTS**

#### LEGAL MATTERS
Cooley LLP, San Diego, California, which has acted as our counsel in connection with this offering, will pass on certain legal matters with respect to U.S. federal law in connection with this offering. Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C., New York, New York has acted as counsel to the agent in connection with this offering.

#### EXPERTS
The Company's consolidated financial statements as of December 31, 2021 and 2020 and for the years then ended and management's assessment of the effectiveness of internal control over financial reporting as of December 31, 2021 incorporated in this prospectus and in the registration statement of which this prospectus forms a part have been so incorporated in reliance on the reports of BDO USA, LLP, an independent registered public accounting firm, incorporated herein by reference, given on the authority of said firm as experts in auditing and accounting.

#### WHERE YOU CAN FIND ADDITIONAL INFORMATION
This prospectus supplement and the accompanying prospectus are part of the registration statement on Form S-3 we filed with the SEC under the Securities Act and do not contain all of the information set forth or incorporated by reference in the registration statement and the exhibits to the registration statement. For further information with respect to us and the securities we are offering under this prospectus supplement, we refer you to the registration statement and the exhibits and schedules filed as a part of the registration statement. We file annual, quarterly and current reports, proxy statements and other information with the SEC. The SEC maintains a website that contains reports, proxy and information statements and other information regarding issuers that file electronically with the SEC, including Bionano. The address of the SEC website is www.sec.gov.

We maintain a website at www.bionanogenomics.com. Information contained in or accessible through our website does not constitute a part of this prospectus supplement or the accompanying prospectus.

S-12<br>

------

#### **TABLE OF CONTENTS**

#### INCORPORATION OF CERTAIN INFORMATION BY REFERENCE
The SEC allows us to "incorporate by reference" information into this prospectus supplement, which means that we can disclose important information to you by referring you to another document filed separately with the SEC. The SEC file number for the documents incorporated by reference in this prospectus supplement is 001-38613. The documents incorporated by reference into this prospectus supplement contain important information about us that you should read.

The following documents are incorporated by reference into this document:

&nbsp;&nbsp;&nbsp;&nbsp;• our Annual Report on Form 10-K for the year ended December 31, 2021, filed with the SEC on [March 1, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000007/bngo-20211231.htm) ;

&nbsp;&nbsp;&nbsp;&nbsp;• our Quarterly Reports on Form 10-Q for the quarters ended March 31, 2022, June 30, 2022 and September 30, 2022 filed with the SEC on [May 5, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000013/bngo-20220331.htm) , [August 4, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000021/bngo-20220630.htm) and [November 3, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000141169022000029/bngo-20220930.htm) , respectively;

&nbsp;&nbsp;&nbsp;&nbsp;• certain portions of our Definitive Proxy Statement on Schedule 14A specifically incorporated by reference into our Annual Report on Form 10-K for the year ended December 31, 2021 (other than information furnished rather than filed), filed with the SEC on [April 27, 2022](https://www.sec.gov/Archives/edgar/data/1411690/000114036122016251/ny20002836x1_def14a.htm) ;

&nbsp;&nbsp;&nbsp;&nbsp;• our Current Reports on Form 8-K (other than information furnished rather than filed) filed with the SEC on [February 23, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122006392/brhc10034332_8k.htm) , [June 10, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122022621/brhc10038653_8k.htm) , [November 18, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122042327/brhc10044406_8k.htm) , [November 28, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122043313/brhc10044740_form8k.htm) , [November 29, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122043393/brhc10044743_8k.htm) , [November 30, 2022](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036122043729/brhc10044882_8k.htm) , and [February 3, 2023](https://www.sec.gov/ix?doc=/Archives/edgar/data/1411690/000114036123004345/brhc10047533_8k.htm) to the extent the information in such reports is filed and not furnished; and

&nbsp;&nbsp;&nbsp;&nbsp;• the description of our common stock in our registration statement on Form 8-A, which was filed with the SEC on [August 17, 2018](https://www.sec.gov/Archives/edgar/data/1411690/000119312518251675/d610675d8a12ba.htm) , including all amendments and reports filed for the purpose of updating such description, including Exhibit 4.12 Annual Report on Form 10-K for the year ended December 31, 2021.

Notwithstanding the statements in the preceding paragraphs, no document, report or exhibit (or portion of any of the foregoing) or any other information that we have "furnished" to the SEC pursuant to the Exchange Act shall be incorporated by reference into this prospectus supplement.

We also incorporate by reference into this prospectus supplement all documents (other than current reports furnished under Item 2.02 or Item 7.01 of Form 8-K and exhibits filed on such form that are related to such items) that are filed by us with the SEC pursuant to Sections 13(a), 13(c), 14 or 15(d) of the Exchange Act (i) after the date of the initial filing of the registration statement of which this prospectus supplement forms a part and prior to effectiveness of the registration statement, and (ii) after the effectiveness of the registration statement but prior to the termination of all offerings of securities covered by this prospectus supplement. These documents include periodic reports, such as Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q and Current Reports on Form 8-K, as well as proxy statements.

We will provide to each person, including any beneficial owner, to whom a prospectus is delivered, without charge upon written or oral request, a copy of any or all of the documents that are incorporated by reference into this prospectus supplement but not delivered with this prospectus supplement, including exhibits which are specifically incorporated by reference into such documents. You should direct any requests for documents to Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100, San Diego, California 92121; telephone: (858) 888-7600.

Any statement contained herein or in a document incorporated or deemed to be incorporated by reference into this document will be deemed to be modified or superseded for purposes of the document to the extent that a statement contained in this document or any other subsequently filed document that is deemed to be incorporated by reference into this document modifies or supersedes the statement.

S-13<br>

------

#### **TABLE OF CONTENTS**

### $200,000,000
![](logo_bionanox2.jpg)<br>

### Common Stock

#### PROSPECTUS SUPPLEMENT

### TD COWEN

#### March 9, 2023
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

------

#### **TABLE OF CONTENTS**

#### PART II

#### INFORMATION NOT REQUIRED IN PROSPECTUS

---

| | |
|:---|:---|
| **Item 14.**<br>| **Other Expenses of Issuance and Distribution.** |

---

The following table sets forth the estimated costs and expenses, other than underwriting discounts and commissions, payable by us in connection with the offering of the securities being registered. All the amounts shown are estimates, except for the SEC registration fee.

---

| | |
|:---|:---|
| &nbsp;&nbsp;SEC registration fee | $11594 |
| FINRA filing fee | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\* |
| Accounting fees and expenses | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\* |
| Legal fees and expenses | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\* |
| Transfer agent and registrar fees and expenses | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\* |
| Trustee fees and expenses | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\* |
| Printing and miscellaneous expenses | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\* |
| Total | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;$\* |

---

\* The amount of securities and number of offerings are indeterminable and the expenses cannot be estimated at this time. An estimate of the aggregate expenses in connection with the sale and distribution of securities being offered will be included in the applicable prospectus supplement.

---

| | |
|:---|:---|
| **Item 15.**<br>| **Indemnification of Directors and Officers.** |

---

We are incorporated under the laws of the State of Delaware. Section 145 of the General Corporation Law of the State of Delaware provides that a Delaware corporation may indemnify any persons who were, are, or are threatened to be made, parties to any threatened, pending or completed action, suit or proceeding, whether civil, criminal, administrative or investigative (other than an action by or in the right of such corporation), by reason of the fact that such person is or was an officer, director, employee or agent of such corporation, or is or was serving at the request of such corporation as an officer, director, employee or agent of another corporation or enterprise. The indemnity may include expenses (including attorneys' fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with such action, suit or proceeding, provided that such person acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the corporation's best interests and, with respect to any criminal action or proceeding, had no reasonable cause to believe that his or her conduct was illegal. A Delaware corporation may indemnify any persons who were, are, or are threatened to be made, a party to any threatened, pending or completed action or suit by or in the right of the corporation by reason of the fact that such person is or was a director, officer, employee or agent of such corporation, or is or was serving at the request of such corporation as a director, officer, employee or agent of another corporation or enterprise. The indemnity may include expenses (including attorneys' fees) actually and reasonably incurred by such person in connection with the defense or settlement of such action or suit provided such person acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the corporation's best interests except that no indemnification is permitted without judicial approval if the officer or director is adjudged to be liable to the corporation. Where an officer or director is successful on the merits or otherwise in the defense of any action referred to above, the corporation must indemnify him or her against the expenses (including attorneys' fees) actually and reasonably incurred.

Our amended and restated certificate of incorporation, as amended, and amended and restated bylaws provide for the indemnification of our directors and officers to the fullest extent permitted under the General Corporation Law of the State of Delaware. Section 102(b)(7) of the General Corporation Law of the State of Delaware permits a corporation to provide in its certificate of incorporation that a director or officer of the corporation shall not be personally liable to the corporation or its stockholders for monetary damages for breach of fiduciary duties as a director or officer, except for liability for any:

&nbsp;&nbsp;&nbsp;&nbsp;• transaction from which the director or officer derives an improper personal benefit;

&nbsp;&nbsp;&nbsp;&nbsp;• act or omission not in good faith or that involves intentional misconduct or a knowing violation of law;

&nbsp;&nbsp;&nbsp;&nbsp;• in the case of a director, unlawful payment of dividends or redemption of shares;

II-1<br>

------

#### **TABLE OF CONTENTS**
&nbsp;&nbsp;&nbsp;&nbsp;• breach of a director's duty of loyalty to the corporation or its stockholders; or

&nbsp;&nbsp;&nbsp;&nbsp;• in the case of an officer, action by or in the right of the corporation.

Our amended and restated certificate of incorporation, as amended, includes such a provision with respect to our directors. Expenses incurred by any officer or director in defending any such action, suit or proceeding in advance of its final disposition will be paid by us upon delivery to us of an undertaking, by or on behalf of such director or officer, to repay all amounts so advanced if it shall ultimately be determined that such director or officer is not entitled to be indemnified by us.

Section 174 of the General Corporation Law of the State of Delaware provides, among other things, that a director who willfully or negligently approves of an unlawful payment of dividends or an unlawful stock purchase or redemption, may be held liable for such actions. A director who was either absent when the unlawful actions were approved or dissented at the time may avoid liability by causing his or her dissent to such actions to be entered in the books containing minutes of the meetings of the board of directors at the time such action occurred or immediately after such absent director receives notice of the unlawful acts.

As permitted by the General Corporation Law of the State of Delaware, we have entered, and continue to enter, into separate indemnity agreements with each of our directors and executive officers that require us to indemnify such persons against any and all costs and expenses (including attorneys', witness or other professional fees) actually and reasonably incurred by such persons in connection with any action, suit or proceeding (including derivative actions), whether actual or threatened, to which any such person may be made a party by reason of the fact that such person is or was a director or officer or is or was acting or serving as an officer, director, employee or agent of ours or any of our affiliated enterprises. Under these agreements, we are not required to provide indemnification for certain matters, including:

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification beyond that permitted by the General Corporation Law of the State of Delaware;

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification for any proceeding with respect to the unlawful payment of remuneration to the director or officer;

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification for certain proceedings involving a final judgment that the director or officer is required to disgorge profits from the purchase or sale of our stock;

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification for proceedings involving a final judgment that the director's or officer's conduct was in bad faith, knowingly fraudulent or deliberately dishonest or constituted willful misconduct or a breach of his or her duty of loyalty, but only to the extent of such specific determination;

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification for proceedings or claims brought by an officer or director against us or any of our directors, officers, employees or agents, except for (1) claims to establish a right of indemnification or proceedings, (2) claims approved by our board of directors, (3) claims required by law, (4) when there has been a change of control as defined in the indemnification agreement with each director or officer, or (5) by us in our sole discretion pursuant to the powers vested to us under the General Corporation Law of the State of Delaware;

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification for settlements the director or officer enters into without our consent; or

&nbsp;&nbsp;&nbsp;&nbsp;• indemnification in violation of any undertaking required by the Securities Act or in any registration statement we file.

The indemnification agreements also set forth certain procedures that will apply in the event of a claim for indemnification thereunder.

We have an insurance policy in place that covers our officers and directors with respect to certain liabilities, including liabilities arising under the Securities Act or otherwise.

Pursuant to certain underwriting agreements we may enter, the underwriters are obligated, under some circumstances, to indemnify our directors, officers and controlling persons against specified liabilities, including liabilities under the Securities Act.

II-2<br>

------

---

| | |
|:---|:---|
| **Item 16.**<br>| **Exhibits.** |

---

---

| | |
|:---|:---|
| **Exhibit** <br>**Number** | **Description** |
| 1.1\* | Form of Underwriting Agreement. |
| [1.2](https://www.sec.gov/Archives/edgar/data/1411690/000114036121009777/nt10022040x3_ex1-1.htm) | Sales Agreement, dated March 23, 2021, by and between the Company and Cowen and Company, LLC (incorporated by reference to Exhibit 1.1 of the Registrant's Current Report on Form 8-K, filed with the SEC on March 24, 2021). |
| [1.3](ny20008078x1_ex1-3.htm) | Amendment No. 1 to Sales Agreement, dated March 9, 2023, by and between the Company and Cowen and Company, LLC. |
| [3.1](https://www.sec.gov/Archives/edgar/data/1411690/000141169021000004/ex31-arcertificateofincorp.htm) | Amended and Restated Certificate of Incorporation, as amended (incorporated by reference to Exhibit 4.1 of the Registrant's Annual Report on Form 10-K, filed with the SEC on March 23, 2021). |
| [3.2](https://www.sec.gov/Archives/edgar/data/1411690/000119312518257763/d607608dex32.htm) | Amended and Restated Bylaws. (incorporated by reference to Exhibit 3.2 of the Registrant's Current Report on Form 8-K, filed with the SEC on August 24, 2018). |
| 4.1 | Reference is made to Exhibits [3.1](https://www.sec.gov/Archives/edgar/data/1411690/000141169021000004/ex31-arcertificateofincorp.htm) and [3.2](https://www.sec.gov/Archives/edgar/data/1411690/000119312518257763/d607608dex32.htm). |
| [4.2](https://www.sec.gov/Archives/edgar/data/1411690/000119312518219135/d782664dex41.htm) | Form of Common Stock Certificate (incorporated by reference to Exhibit 4.1 of the Registrant's Registration Statement on Form S-1 (File No. 333-225970), as amended). |
| [4.3](https://www.sec.gov/Archives/edgar/data/1411690/000119312518217313/d782664dex48.htm) | Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust (incorporated by reference to Exhibit 4.8 of the Registrant's Registration Statement on Form S-1 (File No. 333-225970), as amended). |
| [4.4](https://www.sec.gov/Archives/edgar/data/1411690/000119312518249108/d572381dex11.htm) | Form of Warrant to Purchase Common Stock Issued to Underwriters (attached to Underwriting Agreement) (incorporated by reference to Exhibit 4.9 of the Registrant's Registration Statement on Form S-1 (File No. 333-225970), as amended). |
| [4.5](https://www.sec.gov/Archives/edgar/data/1411690/000119312518249108/d572381dex411.htm) | Form of Warrant Certificate (included in Exhibit 4.6 below) (incorporated by reference to Exhibit 4.11 of the Registrant's Registration Statement on Form S-1 (File No. 333-225970), as amended). |
| [4.6](https://www.sec.gov/Archives/edgar/data/1411690/000119312518249108/d572381dex411.htm) | Form of Warrant Agent Agreement by and between the Registrant and American Stock Transfer & Trust Company LLC, as warrant agent (incorporated by reference to Exhibit 4.11 of the Registrant's Registration Statement on Form S-1 (File No. 333-225970), as amended). |
| [4.7](https://www.sec.gov/Archives/edgar/data/1411690/000119312518332353/d635375dex41.htm) | Form of Warrant to Purchase Common Stock for Service Providers (incorporated by reference to Exhibit 4.1 of the Registrant's Current Report on Form 8-K, filed with the SEC on November 21, 2018). |
| [4.8](https://www.sec.gov/Archives/edgar/data/1411690/000119312519074842/d700738dex43.htm) | Registration Rights Agreement, dated March 14, 2019, by and among the Company and the Innovatus Investors (incorporated by reference to Exhibit 4.1 of the Registrant's Current Report on Form 8-K, filed with the SEC on March 14, 2019).  |
| [4.9](https://www.sec.gov/Archives/edgar/data/1411690/000114036119016923/nt10004193x3_ex4-13.htm) | Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering (incorporated by reference to Exhibit 4.13 of the Registrant's Registration Statement on Form S-1 (File No. 333-233828), as amended). |
| [4.10](https://www.sec.gov/Archives/edgar/data/1411690/000114036120006739/nt10007734x2_ex4-16.htm) | Form of Warrant to Purchase Common Stock issued to Investors in April 2020 Public Offering (incorporated by reference to Exhibit 4.16 of the Registrant's Registration Statement on Form S-1 (File No. 333-237074), as amended). |
| 4.11\* | Specimen Preferred Stock Certificate and Form of Certificate of Designation of Preferred Stock. |
| [4.12](https://www.sec.gov/Archives/edgar/data/1411690/000114036121001447/nt10019031x2_ex4-21.htm) | Form of Debt Indenture (incorporated by reference to Exhibit 4.21 of the Registrant's Automatic Shelf Registration Statement on Form S-3 (File No. 333-252216), filed with the SEC on January 19, 2021). |
| 4.13\* | Form of Debt Securities. |
| [4.14](https://www.sec.gov/Archives/edgar/data/1411690/000114036121001447/nt10019031x2_ex4-23.htm) | Form of Common Stock Warrant Agreement and Warrant Certificate (incorporated by reference to Exhibit 4.23 of the Registrant's Automatic Shelf Registration Statement on Form S-3 (File No. 333- 252216), filed with the SEC on January 19, 2021). |
| [4.15](https://www.sec.gov/Archives/edgar/data/1411690/000114036121001447/nt10019031x2_ex4-24.htm) | Form of Preferred Stock Warrant Agreement and Warrant Certificate (incorporated by reference to Exhibit 4.24 of the Registrant's Automatic Shelf Registration Statement on Form S-3 (File No. 333- 252216), filed with the SEC on January 19, 2021). |
| [4.16](https://www.sec.gov/Archives/edgar/data/1411690/000114036121001447/nt10019031x2_ex4-25.htm) | Form of Debt Securities Warrant Agreement and Warrant Certificate (incorporated by reference to Exhibit 4.25 of the Registrant's Automatic Shelf Registration Statement on Form S-3 (File No. 333- 252216), filed with the SEC on January 19, 2021). |
| [5.1](ny20008078x1_ex5-1.htm) | Opinion of Cooley LLP. |
| [23.1](ny20008078x1_ex23-1.htm) | Consent of BDO USA LLP, independent registered public accounting firm. |

---

II-3<br>

------

---

| | |
|:---|:---|
| **Exhibit** <br>**Number** | **Description** |
| [23.2](ny20008078x1_ex5-1.htm) | Consent of Cooley LLP (included in Exhibit 5.1). |
| [24.1](#tPOA) | Power of Attorney (included on signature page). |
| 25.1\*\* | Statement of Eligibility of Trustee under the Debt Indenture. |
| [107](ny20008078x1_ex107.htm) | Filing Fee Table |

---

\*<br> To be filed by amendment or as an exhibit to a Current Report on Form 8-K and incorporated herein by reference, if applicable.

\*\*<br> To be filed in accordance with the requirements of Section 305(b)(2) of the Trust Indenture Act of 1939, as amended, and the applicable rules thereunder.

---

| | |
|:---|:---|
| **Item 17.**<br>| **Undertakings.** |

---

The undersigned registrant hereby undertakes:

(1)<br> To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

(i)<br> To include any prospectus required by Section 10(a)(3) of the Securities Act;

(ii) To reflect in the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in the registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of prospectus filed with the SEC pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20 percent change in the maximum aggregate offering price set forth in the "Calculation of Registration Fee" table in the effective registration statement; and

(iii)<br> To include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the registration statement;

*provided, however, that the undertakings set forth in paragraphs (1)(i), (1)(ii) and (1)(iii) of this section do not apply if the registration statement is on Form S-3 or Form F-3 and the information required to be included in a post-effective amendment by those paragraphs is contained in reports filed with or furnished to the SEC by the registrant pursuant to Section 13 or Section 15(d) of the Exchange Act that are incorporated by reference in this registration statement or are contained in a form of prospectus filed pursuant to Rule 424(b) that is part of this registration statement.*

(2) That, for the purpose of determining any liability under the Securities Act, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial *bona fide* offering thereof.

(3)<br> To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

(4)<br> That, for the purpose of determining liability under the Securities Act to any purchaser:

(i)<br> Each prospectus filed by the registrant pursuant to Rule 424(b)(3) shall be deemed to be part of the registration statement as of the date the filed prospectus was deemed part of and included in the registration statement; and

(ii) Each prospectus required to be filed pursuant to Rule 424(b)(2), (b)(5), or (b)(7) as part of a registration statement in reliance on Rule 430B relating to an offering made pursuant to Rule 415(a)(1)(i), (vii), or (x) for the purpose of providing the information required by Section 10(a) of the Securities Act shall be deemed to be part of and included in the registration statement as of the earlier of the date such form of prospectus is first used after effectiveness or the date of the first contract of sale of securities in the offering described in the prospectus. As provided in Rule 430B, for liability purposes of the issuer and any person that is at that date an underwriter, such date shall be deemed to be a new effective date of the registration statement relating to the securities in the 

II-4<br>

------

registration statement to which that prospectus relates, and the offering of such securities at that time shall be deemed to be the initial *bona fide* offering thereof. *Provided, however*, that no statement made in a registration statement or prospectus that is part of the registration statement or made in a document incorporated or deemed incorporated by reference into the registration statement or prospectus that is part of the registration statement will, as to a purchaser with a time of contract of sale prior to such effective date, supersede or modify any statement that was made in the registration statement or prospectus that was part of the registration statement or made in any such document immediately prior to such effective date.

(5) That, for the purpose of determining liability of the registrant under the Securities Act to any purchaser in the initial distribution of the securities, the undersigned registrant undertakes that in a primary offering of securities of the undersigned registrant pursuant to this registration statement, regardless of the underwriting method used to sell the securities to the purchaser, if the securities are offered or sold to such purchaser by means of any of the following communications, the undersigned registrant will be a seller to the purchaser and will be considered to offer or sell such securities to such purchaser: (i) any preliminary prospectus or prospectus of the undersigned registrant relating to the offering required to be filed pursuant to Rule 424; (ii) any free writing prospectus relating to the offering prepared by or on behalf of the undersigned registrant or used or referred to by the undersigned registrant; (iii) the portion of any other free writing prospectus relating to the offering containing material information about the undersigned registrant or its securities provided by or on behalf of the undersigned registrant; and (iv) any other communication that is an offer in the offering made by the undersigned registrant to the purchaser.

(6) That, for purposes of determining any liability under the Securities Act, each filing of the registrant's annual report pursuant to Section 13(a) or 15(d) of the Exchange Act (and, where applicable, each filing of an employee benefit plan's annual report pursuant to Section 15(d) of the Exchange Act) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial *bona fide* offering thereof.

(7) Insofar as indemnification for liabilities arising under the Securities Act may be permitted to directors, officers and controlling persons of the registrant pursuant to the foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the SEC such indemnification is against public policy as expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue. 

(8)<br> To file an application for the purpose of determining the eligibility of the trustee to act under subsection (a) of Section 310 of the Trust Indenture Act in accordance with the rules and regulations prescribed by the SEC under Section 305(b)(2) of the Trust Indenture Act.

II-5<br>

------

#### SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of San Diego, State of California, on the 9th day of March, 2023.

---

| | |
|:---|:---|
| **BIONANO GENOMICS, INC.** | **BIONANO GENOMICS, INC.** |
| By: | /s/ R. Erik Holmlin, Ph.D. |
|  | R. Erik Holmlin, Ph.D. <br>*President and Chief Executive Officer* |

---

Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration Statement has been signed by the following persons in the capacities and on the dates indicated.

---

| | | |
|:---|:---|:---|
| **Signature** | **Title** | **Date** |
| /s/ R. Erik Holmlin, Ph.D. | President, Chief Executive Officer and Director <br>*(Principal Executive Officer)* | March 9, 2023 |
| R. Erik Holmlin, Ph.D. | President, Chief Executive Officer and Director <br>*(Principal Executive Officer)* |  |
| /s/ Christopher Stewart | Chief Financial Officer <br>*(Principal Financial and Accounting Officer)* | March 9, 2023 |
| Christopher Stewart | Chief Financial Officer <br>*(Principal Financial and Accounting Officer)* |  |
| \* | Director | March 9, 2023 |
| David L. Barker, Ph.D. |  |  |
| \* | Director | March 9, 2023 |
| Yvonne Linney, Ph.D. |  |  |
| \* | Director | March 9, 2023 |
| Albert A. Luderer, Ph.D. |  |  |
| \* | Director | March 9, 2023 |
| Hannah Mamuszka |  |  |
| \* | Director | March 9, 2023 |
| Aleksandar Rajkovic, M.D., Ph.D. |  |  |
| \* | Director | March 9, 2023 |
| Christopher Twomey |  |  |
| \* | Director | March 9, 2023 |
| Kristiina Vuori, M.D., Ph.D. |  |  |
| /s/ Vincent Wong, J.D., M.B.A. | Director | March 9, 2023 |
| Vincent Wong, J.D., M.B.A. |  |  |

---

---

| | | |
|:---|:---|:---|
| \* | By: | /s/ R. Erik Holmlin, Ph.D. |
|  |  | R. Erik Holmlin, Ph.D. |
|  |  | Attorney-in-Fact<br>|

---

II-6<br>

## Exhibit 1.3

------

**Exhibit 1.3**<br>  

<br> #### AMENDMENT NO. 1 TO

#### SALES AGREEMENT

#### March 9, 2023

This Amendment No. 1 ("**Amendment No. 1**") amends that certain Sales Agreement, dated as of March 23, 2021 (the "**Agreement**"), by and between Bionano Genomics, Inc. (the "**Company**") and Cowen and Company, LLC, as sales agent (the "**Agent**"). Defined terms used herein and not otherwise defined shall have the meaning assigned to such terms in the Agreement.

WITNESSETH THAT:

WHEREAS, Section 15 of the Agreement permits the Company and the Agent to amend the Agreement;

WHEREAS, the Company will not be a "well-known seasoned issuer" as such term is defined in Rule 405 under the Securities Act of 1933, as amended, upon the filing of the Annual Report on Form 10-K for the year ended December 31, 2022; and

WHEREAS, the Company and the Agent now desire to amend the Agreement as provided herein.

NOW, THEREFORE, in consideration of the foregoing premises and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Company and the Agent agree as follows:

1. <u>Section 1</u> of the Agreement is amended by replacing the first sentence of the first paragraph with: "The Company agrees that, from time to time during the term of this Agreement, on the terms and subject to the conditions set forth herein and any Terms Agreement (defined below), it may issue and sell to or through Cowen, acting as agent and/or principal, shares (the "**<u>Shares</u>**") of the Company's common stock, par value $0.0001 per share (the "**<u>Common Stock</u>**"); *provided*, *however*, that in no event shall the Company issue or sell through Cowen such number or dollar amount of Shares that would (a) exceed the number of authorized but unissued shares of Common Stock (less shares of Common Stock issuable upon exercise, conversion or exchange of any outstanding securities of the Company or otherwise reserved from the Company's authorized capital stock), (b) exceed the number or dollar amount of shares of Common Stock permitted to be sold under Form S-3 (including General Instruction I.B.6 thereof, if applicable) or (c) exceed the number or dollar amount of shares of Common Stock for which the Company has filed a Prospectus Supplement (defined below) (the lesser of (a), (b) and (c), the "**<u>Maximum Amount</u>**")."

2. <u>Section 1</u> of the Agreement is further amended by replacing the first sentence of the second paragraph with: "The Company has filed or will file, in accordance with the provisions of the Securities Act of 1933, as amended, and the rules and regulations thereunder (collectively, the "**<u>Securities Act</u>**"), with the Commission a shelf registration statement on Form S-3, including a base prospectus, relating to certain securities, including the Common Stock, to be issued from time to time by the Company, and which incorporates by reference documents that the Company has filed or will file in accordance with the provisions of the Securities Exchange Act of 1934, as amended, and the rules and regulations thereunder (collectively, the "**<u>Exchange Act</u>**").''

------

3. <u>Section 1</u> of the Agreement is further amended by adding the following to paragraph two immediately after the third sentence: "The Company may file one or more additional registration statements from time to time that will contain a base prospectus and related prospectus or prospectus supplement, if applicable (which shall be a Prospectus Supplement), with respect to the Shares.

4. <u>Section 6(a)</u> of the Agreement is amended by (i) deleting the first sentence thereof in its entirety and replacing it with "The Registration Statement has been filed, or any successor Registration Statement will be filed, with the Commission and has been declared effective by the Commission under the Securities Act or, in the case of a successor Registration Statement, will be declared effective by the Commission under the Securities Act prior to the issuance of any Placement Notice by the Company." and (ii) deleting the fourth sentence of such section in its entirety.

5. <u>Section 6(b)</u> of the Agreement is amended and restated in its entirety as set forth below:

[Reserved.]

6. A new <u>Section 20</u> is added to the Agreement as set forth below:

<u>Recognition of the U.S. Special Resolution Regimes</u>. In the event that Cowen is a Covered Entity and becomes subject to a proceeding under a U.S. Special Resolution Regime, the transfer from Cowen of this Agreement, and any interest and obligation in or under this Agreement, will be effective to the same extent as the transfer would be effective under the U.S. Special Resolution Regime if this Agreement, and any such interest and obligation, were governed by the laws of the United States or a state of the United States.

In the event that Cowen is a Covered Entity and Cowen or a BHC Act Affiliate of Cowen becomes subject to a proceeding under a U.S. Special Resolution Regime, Default Rights under this Agreement that may be exercised against Cowen are permitted to be exercised to no greater extent than such Default Rights could be exercised under the U.S. Special Resolution Regime if this Agreement were governed by the laws of the United States or a state of the United States.

For purposes of this Agreement, (A) "**<u>BHC Act Affiliate</u>**" has the meaning assigned to the term "affiliate" in, and shall be interpreted in accordance with, 12 U.S.C. Sec. 1841(k); (B) "**<u>Covered Entity</u>**" means any of the following: (i) a "covered entity" as that term is defined in, and interpreted in accordance with, 12 C.F.R. Sec. 252.82(b); (ii) a "covered bank" as that term is defined in, and interpreted in accordance with, 12 C.F.R. Sec. 47.3(b); or (iii) a "covered FSI" as that term is defined in, and interpreted in accordance with, 12 C.F.R. Sec. 382.2(b); (C) "**<u>Default Right</u>**" has the meaning assigned to that term in, and shall be interpreted in accordance with, §§12 C.F.R. 252.81, 47.2 or 382.1, as applicable; and (D) "**<u>U.S. Special Resolution Regime</u>**" means each of (i) the Federal Deposit Insurance Act and the regulations promulgated thereunder and (ii) Title II of the Dodd-Frank Wall Street Reform and Consumer Protection Act and the regulations promulgated thereunder.

7. References to the date of the Agreement in the form of Placement Notice included as Schedule 1 to the Agreement are hereby revised to read, "March 23, 2021, as amended by Amendment No. 1 thereto, dated March 9, 2023."

8. This Amendment No. 1 shall be deemed effective on the date first set forth above.

------

9. Except as amended hereby, the Agreement as now in effect is ratified and confirmed hereby in all respects. For the avoidance of doubt, this Amendment No. 1 and all of its provisions shall be deemed to be a part of the Agreement, as amended hereby. The Agreement as amended by this Amendment No. 1 constitutes the entire agreement of the parties hereto and supersedes all prior written or oral and all contemporaneous oral agreements, understandings and negotiations with respect to the subject matter hereof and thereof.

10. This Amendment No. 1 shall be governed by and construed in accordance with the internal laws of the State of New York applicable to agreements made and to be performed in such state. Any legal suit, action or proceeding arising out of or based upon this Amendment No. 1 or the transactions contemplated hereby may be instituted in the federal courts of the United States of America located in the Borough of Manhattan in the City of New York or the courts of the State of New York in each case located in the Borough of Manhattan in the City of New York (collectively, the "**Specified Courts**"), and each party irrevocably submits to the exclusive jurisdiction (except for proceedings instituted in regard to the enforcement of a judgment of any such court, as to which such jurisdiction is non-exclusive) of such courts in any such suit, action or proceeding. Service of any process, summons, notice or document by mail to such party's address set forth in the Agreement shall be effective service of process for any suit, action or other proceeding brought in any such court. The parties irrevocably and unconditionally waive any objection to the laying of venue of any suit, action or other proceeding in the Specified Courts and irrevocably and unconditionally waive and agree not to plead or claim in any such court that any such suit, action or other proceeding brought in any such court has been brought in an inconvenient forum.

*[Signature page follows.]*

------

If the foregoing is in accordance with your understanding of our agreement, kindly sign and return to the Company the enclosed copies hereof, whereupon this instrument, along with all counterparts hereof, shall become a binding agreement in accordance with its terms.

---

| | |
|:---|:---|
| Very truly yours, | Very truly yours, |
| **BIONANO GENOMICS, INC.**<br> ****  | **BIONANO GENOMICS, INC.**<br> ****  |
| By: | /s/ R. Erik Holmlin, Ph.D. |
| Name: | R. Erik Holmlin, Ph.D. |
| Title: | President and Chief Executive Officer |

---

The foregoing Amendment is hereby confirmed and accepted by the Agent in New York, New York as of the date first above written.

#### COWEN AND COMPANY, LLC

---

| | |
|:---|:---|
| By: | /s/ Michael Murphy |
| Name: | Michael Murphy |
| Title: | Managing Director |

---

------

## Exhibit 5.1

------

**Exhibit 5.1**<br>

![](logo_cooley.jpg)

Thomas A. Coll

+1 858 550 6013

collta@cooley.com

March 9, 2023

Bionano Genomics, Inc.

9540 Towne Centre Drive, Suite 100

San Diego, CA 92121

Ladies and Gentlemen:

We have acted as counsel to Bionano Genomics, Inc., a Delaware corporation (the "***Company***"), in connection with the filing of Post-Effective Amendment No. 1 to the Registration Statement on Form S-3 (File No. 333-252216) (as so amended, the "***Registration Statement***") with the Securities and Exchange Commission (the "***Commission***") by the Company under the Securities Act of 1933, as amended (the "***Securities Act***"). The Registration Statement includes two prospectuses: (i) a base prospectus (the "***Base Prospectus***") that provides it will be supplemented in the future by one or more prospectus supplements (each, a "***Prospectus Supplement***") and (ii) a sales agreement prospectus (the "***Sales Agreement Prospectus***"), covering up to $200,000,000 of shares (the "***Sales Agreement Shares***") of common stock, par value $0.0001 per share, of the Company ("***Common Stock***") that may be sold by the Company pursuant to that certain Sales Agreement, dated March 23, 2021, by and between the Company and Cowen and Company, LLC (the "***Sales Agreement***"). The Registration Statement, including the Base Prospectus (as supplemented from time to time by one or more Prospectus Supplements) and the Sales Agreement Prospectus, will provide for the registration by the Company of the sale of:

&nbsp;&nbsp;&nbsp;&nbsp;• shares of Common Stock (the "  ***Base Prospectus Shares*** ");

&nbsp;&nbsp;&nbsp;&nbsp;• shares of preferred stock, par value $0.0001 per share, of the Company (the "  ***Preferred Stock*** ");

&nbsp;&nbsp;&nbsp;&nbsp;• debt securities, in one or more series (the "  ***Debt Securities*** "), which may be issued pursuant to an indenture to be dated on or about the date of the first issuance of Debt
 Securities thereunder, by and between a trustee to be selected by the Company (the "  ***Trustee***") and the Company, in the form filed as Exhibit 4.21 to the Registration Statement and
 one or more indentures supplemental thereto with respect to any particular series of Debt Securities (the "  ***Indenture*** ");

&nbsp;&nbsp;&nbsp;&nbsp;• warrants to purchase Common Stock, Preferred Stock or Debt Securities (the "  ***Warrants*** "), which may be issued under one or more warrant agreements, to be dated on or about the
 date of the first issuance of the Warrants thereunder, by and between a warrant agent to be selected by the Company (the "  ***Warrant Agent***") and the Company, in the forms filed as
 Exhibits 4.23, 4.24 and 4.25, respectively, to the Registration Statement (each, a "  ***Warrant Agreement*** "); and

&nbsp;&nbsp;&nbsp;&nbsp;• the Sales Agreement Shares.

Cooley LLP 10265 Science Center Drive San Diego, CA 92121<br> t: (858) 550-6000 f: (858) 550-6420 cooley.com

------

![](logo_cooley.jpg)

March 9, 2023

Page Two

The Base Prospectus Shares, the Preferred Stock, the Debt Securities, the Warrants and the Sales Agreement Shares, plus any additional Common Stock, Preferred Stock, Debt Securities and Warrants that may be registered pursuant to any registration statement that the Company may hereafter file with the Commission pursuant to Rule 462(b) under the Securities Act in connection with an offering by the Company pursuant to the Registration Statement, are collectively referred to herein as the "***Securities***." The Securities are being registered for offer and sale from time to time pursuant to Rule 415 under the Securities Act.

In connection with this opinion, we have examined and relied upon such records, documents, certificates, opinions, memoranda and other instruments as in our judgment are necessary or appropriate to enable us to render the opinion expressed below. As to certain factual matters, we have relied upon a certificate of an officer of the Company and have not independently verified such matters.

In rendering this opinion, we have assumed the genuineness of all signatures; the authenticity of all documents submitted to us as originals; the conformity to originals of all documents submitted to us as copies; the accuracy, completeness and authenticity of certificates of public officials; and the due authorization, execution and delivery of all documents where authorization, execution and delivery are prerequisites to the effectiveness thereof.

With respect to our opinion as to the Base Prospectus Shares, we have assumed that, at the time of issuance and sale, a sufficient number of shares of Common Stock will be authorized and available for issuance and that the consideration for the issuance and sale of the Base Prospectus Shares (or Preferred Stock or Debt Securities convertible into, or Warrants exercisable for, Common Stock) will be in an amount that is not less than the par value of the Common Stock. With respect to our opinion as to the Preferred Stock, we have assumed that, at the time of issuance and sale, a sufficient number of shares of Preferred Stock will be authorized, designated and available for issuance and that the consideration for the issuance and sale of the Preferred Stock (or Debt Securities convertible into, or Warrants exercisable for, Preferred Stock) will be in an amount that is not less than the par value of the Preferred Stock. We have also assumed that any Debt Securities or Warrants offered under the Registration Statement, and the related Indenture and Warrant Agreement, will be executed in the forms filed as exhibits to the Registration Statement or incorporated by reference therein. We have also assumed that (i) with respect to Securities issuable upon conversion of any convertible Preferred Stock, such convertible Preferred Stock will be duly authorized, validly issued, fully paid and nonassessable; and (ii) with respect to any Securities issuable upon conversion of any convertible Debt Securities or upon exercise of any Warrants, such convertible Debt Securities or Warrants will constitute valid and legally binding obligations of the Company, enforceable against the Company in accordance with their terms, except as enforcement may be limited by applicable bankruptcy, insolvency, reorganization, arrangement, moratorium or other similar laws affecting creditors' rights, and subject to general equity principles and to limitations on availability of equitable relief, including specific performance.

------

![](logo_cooley.jpg)

March 9, 2023

Page Three

With respect to the Sales Agreement Shares, we have assumed (i) that each sale of the Sales Agreement Shares will be duly authorized by the Board of Directors of the Company, a duly authorized committee thereof or a person or body pursuant to an authorization granted in accordance with Section 152 of the General Corporation Law of the State of Delaware (the "***DGCL***"), (ii) that no more than 162,601,626 Sales Agreement Shares will be sold under the Sales Agreement pursuant to the Sales Agreement Prospectus and (iii) that the price at which the Sales Agreement Shares are sold will equal or exceed the par value of the Common Stock. We express no opinion to the extent that future issuances of securities of the Company, anti-dilution adjustments to outstanding securities of the Company and/or other matters cause the number of shares of Common Stock then available for issuance under the Sales Agreement to exceed the number of shares of Common Stock then available for issuance by the Company.

Our opinion herein is expressed solely with respect to the DGCL and, as to the Debt Securities and the Warrants constituting valid and legally binding obligations of the Company, the laws of the State of New York. Our opinion is based on these laws as in effect on the date hereof. We express no opinion to the extent that any other laws are applicable to the subject matter hereof and express no opinion and provide no assurance as to compliance with any federal or state securities law, rule or regulation.

On the basis of the foregoing and in reliance thereon, and subject to the qualifications herein stated, we are of the opinion that:

**1.** With respect to the Base Prospectus Shares offered under the Registration Statement, provided that (a) the Registration Statement and any required post-effective amendment thereto have become effective under the Securities Act and the Base Prospectus and any and all Prospectus Supplement(s) required by applicable laws have been delivered and filed as required by such laws; (b) the issuance of the Base Prospectus Shares has been duly authorized by all necessary corporate action on the part of the Company; (c) the issuance and sale of the Base Prospectus Shares do not violate any applicable law, are in conformity with the Company's then operative certificate of incorporation (the "***Certificate of Incorporation***") and bylaws (the "***Bylaws***"), do not result in a default under or breach of any agreement or instrument binding upon the Company and comply with any applicable requirement or restriction imposed by any court or governmental body having jurisdiction over the Company; and (d) the certificates, if any, for the Base Prospectus Shares have been duly executed by the Company, countersigned by the transfer agent therefor and duly delivered to the purchasers thereof against payment therefor, then the Base Prospectus Shares, when issued and sold as contemplated in the Registration Statement, the Base Prospectus and the related Prospectus Supplement(s), and in accordance with a duly authorized, executed and delivered purchase, underwriting or similar agreement, or upon conversion of any convertible Preferred Stock, or convertible Debt Securities in accordance with their terms, or upon exercise of any Warrants in accordance with their terms, will be validly issued, fully paid and nonassessable.

------

![](logo_cooley.jpg)

March 9, 2023

Page Four

**2.** With respect to the Preferred Stock offered under the Registration Statement, provided that (a) the Registration Statement and any required post-effective amendment thereto have become effective under the Securities Act and the Base Prospectus and any and all Prospectus Supplement(s) required by applicable laws have been delivered and filed as required by such laws; (b) the terms and issuance of the Preferred Stock have been duly authorized by all necessary corporate action on the part of the Company; (c) the terms of the shares of the Preferred Stock and their issuance and sale do not violate any applicable law, are in conformity with the Certificate of Incorporation and the Bylaws, do not result in a default under or breach of any agreement or instrument binding upon the Company and comply with any applicable requirement or restriction imposed by any court or governmental body having jurisdiction over the Company; and (d) the certificates, if any, for the Preferred Stock have been duly executed by the Company, countersigned by the transfer agent therefor and duly delivered to the purchasers thereof against payment therefor, then the Preferred Stock, when issued and sold as contemplated in the Registration Statement, the Base Prospectus and the related Prospectus Supplement(s) and in accordance with a duly authorized, executed and delivered purchase, underwriting or similar agreement, or upon conversion of any convertible Debt Securities in accordance with their terms, or upon exercise of any Warrants in accordance with their terms, will be validly issued, fully paid and nonassessable.

**3.** With respect to any series of the Debt Securities issued under the Indenture and offered under the Registration Statement, provided that (a) the Registration Statement and any required post-effective amendment thereto have become effective under the Securities Act and the Base Prospectus and any and all Prospectus Supplement(s) required by applicable laws have been delivered and filed as required by such laws; (b) the Indenture has been duly authorized by the Company and the Trustee by all necessary corporate action; (c) the Indenture in substantially the form filed as an exhibit to the Registration Statement, has been duly executed and delivered by the Company and the Trustee and has been qualified under the Trust Indenture Act of 1939, as amended; (d) the issuance and terms of the Debt Securities have been duly authorized by the Company by all necessary corporate action; (e) the terms of the Debt Securities and of their issuance and sale have been duly established in conformity with the Indenture so as not to violate any applicable law or result in a default under or breach of any agreement or instrument binding upon the Company, so as to be in conformity with the Certificate of Incorporation and the Bylaws, and so as to comply with any requirement or restriction imposed by any court or governmental body having jurisdiction over the Company; and (f) the notes representing the Debt Securities have been duly executed and delivered by the Company and authenticated by the Trustee pursuant to the Indenture and delivered against payment therefor, then the Debt Securities, when issued and sold in accordance with the Indenture and a duly authorized, executed and delivered purchase, underwriting or similar agreement, or upon exercise of any Warrants in accordance with their terms, will be valid and legally binding obligations of the Company, except as may be limited by bankruptcy, insolvency, reorganization, moratorium or other similar laws relating to or affecting creditors' rights generally, and by general equitable principles (regardless of whether considered in a proceeding at law or in equity).

------

![](logo_cooley.jpg)

March 9, 2023

Page Five

**4.** With respect to the Warrants issued under the Warrant Agreements and offered under the Registration Statement, provided that (a) the Registration Statement and any required post-effective amendment thereto have become effective under the Securities Act and the Base Prospectus and any and all Prospectus Supplement(s) required by applicable laws have been delivered and filed as required by such laws; (b) the applicable Warrant Agreement has been duly authorized by the Company and the Warrant Agent by all necessary corporate action; (c) the applicable Warrant Agreement has been duly executed and delivered by the Company and the Warrant Agent; (d) the issuance and terms of the Warrants have been duly authorized by the Company by all necessary corporate action; (e) the terms of the Warrants and of their issuance and sale have been duly established in conformity with the applicable Warrant Agreement and as described in the Registration Statement, the Base Prospectus and the related Prospectus Supplement(s), so as not to violate any applicable law or result in a default under or breach of any agreement or instrument binding upon the Company, so as to be in conformity with the Certificate of Incorporation and the Bylaws, and so as to comply with any requirement or restriction imposed by any court or governmental body having jurisdiction over the Company; and (f) the Warrants have been duly executed and delivered by the Company and authenticated by the Warrant Agent pursuant to the applicable Warrant Agreement and delivered against payment therefor, then the Warrants, when issued and sold as contemplated in the Registration Statement, the Base Prospectus and the Prospectus Supplement(s) and in accordance with the applicable Warrant Agreement and a duly authorized, executed and delivered purchase, underwriting or similar agreement, will be valid and legally binding obligations of the Company, except as may be limited by bankruptcy, insolvency, reorganization, moratorium or other similar laws relating to or affecting creditors' rights generally, and by general equitable principles (regardless of whether considered in a proceeding at law or in equity).

**5.** The Sales Agreement Shares, when sold and issued against payment therefor in accordance with the Sales Agreement, the Registration Statement and the Sales Agreement Prospectus, will be validly issued, fully paid and nonassessable.

\* \* \* \* \*

------

![](logo_cooley.jpg)

March 9, 2023

Page Six<br>

We hereby consent to the filing of this opinion as an exhibit to the Registration Statement and to the reference to our firm under the caption "Legal Matters" in the Base Prospectus and the Sales Agreement Prospectus. We further consent to the incorporation by reference of this opinion into any registration statement filed pursuant to Rule 462(b) under the Securities Act with respect to additional Securities. In giving such consent, we do not thereby admit that we are in the category of persons whose consent is required under Section 7 of the Securities Act or the rules and regulations of the Commission thereunder.

Our opinion set forth above is limited to the matters expressly set forth in this letter, and no opinion is implied or may be inferred beyond the matters expressly stated. This opinion speaks only as to law and facts in effect or existing as of the date hereof, and we undertake no obligation or responsibility to update or supplement this opinion to reflect any facts or circumstances that may hereafter come to our attention or any changes in law that may hereafter occur.

Sincerely,

Cooley LLP

By: <u>/s/ Thomas A. Coll</u>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

Thomas A. Coll

------

## Exhibit 23.1

------

**Exhibit 23.1**<br>

<u>Consent of Independent Registered Public Accounting Firm</u> <br> We hereby consent to the incorporation by reference in the Prospectus constituting a part of this Registration Statement of our reports dated March 1, 2022, relating to the consolidated financial statements and effectiveness of Bionano Genomics, Inc.'s (the "Company") internal control over financial reporting appearing in the Company's Annual Report on Form 10-K for the year ended December 31, 2021.<br>

We also consent to the reference to us under the caption "Experts" in the Prospectus. <br>

/s/ BDO USA, LLP

San Diego, California

March 9, 2023

------

## Ex-Filing

------

#### Exhibit 107

#### Calculation of Filing Fee Table

#### Form S-3
(Form Type)

#### Bionano Genomics, Inc.
(Exact Name of Registrant as Specified in its Charter)

<u>Table 1: Newly Registered Securities</u>

---

| | | | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|:---|:---|
| | **Security Type** | **Security Class Title** | **Fee Calculation Rule** | **Amount Registered** | **Proposed Maximum Offering Price Per Unit** | **Maximum Aggregate Offering Price** | **Fee Rate** | **Amount of Registration Fee** |
| **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** | **Newly Registered Securities** |
| Fees to Be Paid | Equity | Common Stock, par value $0.0001 per share |  |  |  |  |  |  |
| Fees to Be Paid | Equity | Preferred Stock, par value $0.0001 per share |  |  |  |  |  |  |
| Fees to Be Paid | Debt | Debt Securities |  |  |  |  |  |  |
| Fees to Be Paid | Other | Warrants |  |  |  |  |  |  |
| Fees to Be Paid | Unallocated (Universal) Shelf |  | 457(o) | (1) | (2) | $400000000 | .00011020 | $44080 |
| Fees Previously Paid | Equity | Common Stock, par value $0.0001 per share | 457(o) |  |  | $297766726 | .00010910 | $32486<sup>(3)</sup> |
|  | **Total Offering Amounts** | **Total Offering Amounts** | **Total Offering Amounts** | **Total Offering Amounts** |  | $400000000 |  | $44080 |
|  | **Total Fees Previously Paid** | **Total Fees Previously Paid** | **Total Fees Previously Paid** | **Total Fees Previously Paid** |  |  |  | $32486 |
|  | **Total Fee Offsets** | **Total Fee Offsets** | **Total Fee Offsets** | **Total Fee Offsets** |  |  |  |  |
|  | **Net Fee Due** | **Net Fee Due** | **Net Fee Due** | **Net Fee Due** |  |  |  | $11594 |

---

------

<sup>(1)</sup> There are being registered hereunder such indeterminate number of shares of common stock, such indeterminate number of shares of preferred stock, such indeterminate principal amount of debt securities and such indeterminate number of warrants to purchase common stock, preferred stock or debt securities as shall have an aggregate initial offering price not to exceed $400,000,000. If any debt securities are issued at an original issue discount, then the principal amount of such debt securities shall be in such greater amount as shall result in an aggregate initial offering price not to exceed $400,000,000, less the aggregate dollar amount of all securities previously issued hereunder. The securities registered also include such indeterminate amount of all securities previously issued hereunder. The securities registered also include such indeterminate number of shares of common stock, preferred stock and amount of debt securities as may be issued upon conversion of or exchange for debt securities that provide for conversion or exchange, upon exercise of warrants or pursuant to the antidilution provisions of any such securities. In addition, pursuant to Rule 416 under the Securities Act of 1933, as amended, or the Securities Act, the shares being registered hereunder include such indeterminate number of shares of common stock and preferred stock as may be issuable with respect to the shares being registered hereunder as a result of stock splits, stock dividends or similar transactions.<br>

<sup>(2)</sup> The proposed maximum aggregate offering price per class of security will be determined from time to time by the registrant in connection with the issuance by the registrant of the securities registered hereunder and is not specified as to each class of security pursuant to Instruction 2.A.iii.b under the heading "Instructions to the Calculation of Filing Fee Tables and Related Disclosure" of Part II, Item 16, of Form S-3 under the Securities Act.<br>

<sup>(3)</sup> The registrant previously paid a fee of $32,486 related to $297,766,726 of the registrant's common stock that may be issued and sold under a sales agreement with Cowen and Company, LLC, which is applied to the registrant's total registration fee.<br>

------