Prepare Library | Sequence | Analyze Data

BaseSpace™ Sequence Hub
Data management and analysis that is simple enough for labs getting started and powerfulenough for rapidly scaling up next-generation sequencing operations.

Highlights• Touchpoint-free automation
Configure analysis workflows and automated quality control
steps to remove touchpoints and streamline data processing• Real-time data upload and run monitoring
View run progress as data uploads to the data repository andbegin analysis immediately after run completes• One-click analysis with over 80 bioinformatics tools
Access a growing collection of bioinformatics tools, including
the DRAGEN™ Bio-IT Platform, easily with BaseSpace Apps• Global collaboration and data sharing
Configure options to disseminate data to peers, create
working groups, or engage the scientific community

Introduction
Next-generation sequencing (NGS) has revolutionized the way and rate
at which biomedical research is conducted. As the cost of sequencing
decreases, the volume of NGS data increases, creating newbottlenecks. The challenges of secure data storage and management,complex data analysis, and sharing results with collaborators canresult in nonuniform methods within institutions and labs, conflicting
results, and increased operational overhead. BaseSpace Sequence
Hub is a genomics cloud computing platform designed to bringsimplified data management and analytical sequencing tools directly toinvestigators in a user-friendly format (Figure 1). BaseSpace Sequence
Hub provides flexibility and convenience with an array of tools,
significantly expanding the possibilities of yielding meaningful resultsfrom NGS data.

Figure 1: Intuitive BaseSpace Sequence Hub dashboard—The Notifications panel has widgets that highlight the latest sharing, ownership transfer activities,occasional alerts on new features, bugs, etc. The Latest Runs panel has widgets that provide real-time status of the sequencing run. The Latest Analyses panel haswidgets that show the status of user app sessions

For Research Use Only. Not for use in diagnostic procedures.

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Prepare Library | Sequence | Analyze Data

Figure 2: Monitor run data in real time—Sequence Analysis Viewer (SAV) capabilities are built into the BaseSpace Sequence Hub user interface, allowing real-time,cycle-by-cycle monitoring. The Charts view shows data by lane and by cycle, with Q-score distribution and heat map features. Each graph can be expanded to full size.

Scalable bioinformatics software

Real-time monitoring

Traditionally, labs pursuing NGS required the services of highly
trained bioinformaticians and a dedicated infrastructure to perform
data management, analysis, and storage. BaseSpace Sequence
Hub relieves many of these burdens by automating bioinformatic
analysis using cloud-based software applications. These push-button
apps were designed with the biologist in mind, enabling users toproduce biologically relevant results from raw data that can be used indownstream analysis tools. All BaseSpace Sequence Hub accounts
come with 1 TB of free storage, but this storage is scalable according
to changing laboratory needs.

BaseSpace Sequence Hub is the only cloud platform directly
integrated with Illumina sequencing systems. With the Runs
Dashboard, users can monitor data, by lane or by cycle, as data
are generated in real time on the sequencer. Additionally, users canview quality performance metrics from the browsers (Figure 2) or on
mobile devices using the BaseSpace Mobile App (Figure 3). Data
are seamlessly pushed to BaseSpace Sequence Hub for automatic
analysis and storage upon run completion, with the option of retaining
data for local hosting and analysis on the instrument.

Run setup and management
BaseSpace Sequence Hub makes biosample and run management
easy using the Prep Tab feature, an intuitive, graphical environment for
one-stop library and run preparation.
••

Prepare and manage biological samples, libraries, pools, andplanned sequencing runs directly in BaseSpace Sequence HubImport biological samples or library information in batch mode forlarge experiments

The features available in Prep Tab allow for easy integration ofBaseSpace Sequence Hub with library preparation and sequencing
platforms. Using the Prep Tab, the entire workflow can be planned
from biosample creation and library preparation to pooling andsequencing. When a run has been planned and is ready to start, noadditional setup is required at the instrument.
•••

Prep Tab supports all Illumina library prep kits
Prep Tab can also be used for custom library kitsMiSeq™, NovaSeq™, and HiSeq™ instruments (including theHiSeq X System) can be set up in BaseSpace Sequence Hubusing sample sheets.

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Figure 3: View runs on the BaseSpace Mobile App—Runs can be viewed
on the BaseSpace Mobile App on any iOS-compatible device. The Mobile App
also provides status updates on analysis, including push-button notifications
when runs and analyses are completed. Download the Mobile App for free at theiTunes app store.

For Research Use Only. Not for use in diagnostic procedures.

Design Content | Prepare Library | Sequence | Analyze Data

BaseSpace Apps, powerful yet simple
Analysis of complex sequencing data sets is a challenge at any scale.
BaseSpace Sequence Hub provides a continuously growing list of
powerful apps (analysis workflows and tools), allowing researchers to
set up and perform complex data analyses. A simple interface links
data sets directly to bioinformatics pipelines based on open source
and commercial tools (Figure 4). BaseSpace Apps meet the diverse
needs of any researcher, regardless of informatics experience, in an
expansive analysis ecosystem.

Develop custom apps to analyze data
Working with customized pipelines and tools within BaseSpace
Sequence Hub simplifies bioinformatics processes by allowing theuser to bring their analysis methods to the data in a flexible platform.
BaseSpace Sequence Hub supports third-party software creation byproviding a robust app development platform. The BaseSpace Native
App Engine and extensive application program interfaces support
development of apps to perform analyses and create custom reports.
Customized apps can be kept private, shared between collaborators,
or made publicly available to all BaseSpace Sequence Hub users.

Streamline analysis with automated workflows
A typical bioinformatics analysis workflow includes many steps(Figure 5). From reviewing lane metrics and post-run demultiplexing tomerging data from multiple runs, setting up secondary analyses, andreviewing results, the process is time-consuming and susceptible tohuman error. BaseSpace Sequence Hub enables users to configure
customized workflows to automate the process from sequencing run

completion to secondary analysis and results review, prior to datadelivery or tertiary analyses.
These features also enable high-volume laboratories to maximize
efficiencies by tracking biosample status throughout the data analysis
workflow, so users can review the progress of individual biosamples as
they proceed down individual analysis paths.

Collaborate better with workgroups
The ability to form a team through the Workgroup feature is available
with an upgrade to a BaseSpace Professional subscription orBaseSpace Enterprise subscription. Each BaseSpace Professional
subscription is provided with a single workgroup, while BaseSpaceEnterprise tier customers can create any number of workgroups forbetter management of access to data. This feature enables simplified
collaboration on a global scale (Figure 6):••••

The team administrator (subscriber) can invite other users tothe Workgroup
All team members will have access with individual login
Team members can switch between individual andWorkgroup spaces
In Workgroup context, team members can access all runs,analyses, and storage usage that belongs to the Workgroup

In large labs with multiple users, accounts and passwords are often
shared between technicians, bioinformaticians, lab managers, etc.
The Workgroup feature enables each invited individual to log in withindividual passwords. This also mitigates issues that may arise when
any user leaves the lab.

Figure 4: Launch analytical tools on demand—Browse and explore a growing list of apps from the bioinformatics community in the BaseSpace Apps Store, andlaunch selected apps with a single click, directly from the data set.

For Research Use Only. Not for use in diagnostic procedures.

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Prepare Library | Sequence | Analyze Data

Figure 5: Automated workflow in BaseSpace Sequence Hub—BaseSpace Sequence Hub enables users to configure customized analysis workflows that include
automatic FASTQ generation, automatic sample aggregation (when applicable), automatic Lane QC, automatic launching of analyses with BaseSpace Apps, andautomated secondary analysis QC.

Figure 7: Global accessibility—Flexible collaboration tools simplify data
sharing, expand collaboration circles, and keep track of who shares data.

of industry-accepted security standards.1 Enterprise subscriptions
offer an additional level of security. Enterprise customers areprovided their own domain and the ability to use their own SAML 2.0
supported authentication service to manage users and passwords.
BaseSpace Sequence Hub also supports Enterprise customers in a
Health Insurance Portability and Accountability Act (HIPAA)-regulated
environment with a Business Associate Agreement (BAA). For more
information about security features, read the BaseSpace Sequence
Hub Security and Privacy white paper.2

Figure 6: Workgroup feature—With Workgroup, users can log in with personalcredentials, then switch context between individual accounts and Workgroupaccounts. In Workgroup context, users can view all runs and analyses commonto the Workgroup, as well as use the storage and computation hours purchasedby the Workgroup, as shown in the different dashboards.

Collaboration on a global scale
Researchers frequently need to collaborate and share access tosequencing data and results. BaseSpace Sequence Hub enables
users to share raw sequencing data and analysis results, easily andsecurely, with collaborators across the globe. Shareable links can beeasily created and emailed to partners, allowing instantaneous accessto shared data and results. Also, data delivery is simplified with theability to transfer runs and projects effortlessly to collaborators orcustomers. BaseSpace Sequence Hub makes big data portable andaccessible to the people who need it most (Figure 7).

Enhanced Security
Security is of paramount importance when making the decision
to move genomic data to cloud-based analysis and storage. InBaseSpace Sequence Hub, data are protected through various
physical, electronic, and administrative measures. Data for upload areencrypted using the AES256 standard and protected by transfer layer
security (TLS). Data within BaseSpace Sequence Hub are hosted on
Amazon Web Services (AWS), which is compliant with a wide variety

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Flexible billing plans
BaseSpace Sequence Hub offers customers the option to use only
what they need, providing both a monthly billing feature for the use of
paid apps and storage, and a prepaid option that allows customers to
pay for storage and apps as they are used. All BaseSpace Sequence
Hub accounts come with 1 TB of free data storage, access to
instrument run monitoring capabilities, and free demultiplexing for runs
streamed into a customer’s account. Log in to BaseSpace Sequence
Hub and visit the app page for more information about apps andpricing. Customers can purchase subscriptions for specified storage
amounts and use the pay-as-you-go and prepaid features for any
additional storage and paid apps. Billing features vary with the type ofsubscription (Table 1). Analysis costs vary based on the input sample
type, parameters selected, and app used. For more information, readthe BaseSpace Apps Quick Guide Handout.
The monthly billing feature in BaseSpace Sequence Hub uses iCredits
to track the use of paid apps and storage. For paid apps, the iCredits
system tracks central processing unit (CPU) cycles used, and app
license fees for a limited number of third-party apps (Figure 8). Eachpaid app using CPU cycles is priced in iCredits per node hour, and istracked in per-minute billing increments. Third-party app license fees
are listed in iCredits and are tracked upon app launch. Any storage
use above baseline is priced at 0.03 iCredits/GB per month, and istracked in per-day billing increments. A bill is sent each month forusage of paid apps and additional storage.

For Research Use Only. Not for use in diagnostic procedures.

Prepare Library | Sequence | Analyze Data
Table 1: Billing features for BaseSpace Sequence Hub subscriptions
FeatureBasic

Professional

Enterprise

Included storage

1 TB

1 TB

1 TB

Complementary iCredits

250500500

Run setup and monitoring

X

X

X

FASTQ generation

Free

Free

Free

Data egress

FreeFreeFree

Data sharing

X

X

X

Advanced security and compliance (encryption, ISO27001, ISO13485)

X

X

X

API and command-line access

X

X

X

Number of users

One

Unlimited

Unlimited

One

Unlimited

Workgroups
Premier security (private domain, single sign-ona, audit trail, accesscontrol)
HIPAA BAA (US only)

X
X

Service level agreement

X

a. Available for systems with control software that support Universal Copy Service. Not available for all legacy systems.

Figure 8: Paid app pricing—Individual apps can be purchased with iCredits on a price-per-node hour basis, single-use fee, or annual subscription fee.

Learn moreReferences

For more details on BaseSpace Sequence Hub, or to sign up for a free
BaseSpace account, visit www.illumina.com/basespace

1.

Ordering information
Product

Catalog no.

Illumina Analytics - 1 iCredit

20042038Illumina Analytics Starter Package - 1000 iCredits

20042039

Illumina Analytics - 5000 iCredits

20042040

Illumina Analytics - 50,000 iCredits

20042041

Illumina Analytics - 100,000 iCredits

20042042

BaseSpace Sequence Hub Professional Annual Subscription

20041109

BaseSpace Sequence Hub Enterprise Annual Subscription

15066411

BaseSpace Sequence Hub Consumption Billing

20012931

2.

AWS Cloud Security. aws.amazon.com/security/. Accessed March 13,2020.
Illumina (2016). BaseSpace Sequence Hub Security and Privacy. AccessedMarch 13, 2020.

Illumina • 1.800.809.4566 toll-free (US) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com© 2020 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark
information, see www.illumina.com/company/legal.html. 970-2011-009-E QB9612

For Research Use Only. Not for use in diagnostic procedures.

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