TITLE: Submitting Genomes
AUTHORS: emma.pearce

[DESCRIPTION]
Steps to submit a genome to NCBI through Bankit 

[STEPS]
SECTION: Submitting to Bankit
1. Log into Bankit with UCSF username and password:
    - Follow this link: https://www.ncbi.nlm.nih.gov/WebSub/?form=history&tool=genbank
    - Choose more login options and select University of California, San Francisco
SECTION: Submitting to Bankit
2. Select "Start Bankit Submission"
SECTION: Submitting to Bankit
3. Fill out the contact information
SECTION: Submitting to Bankit
4. Sequence Authors:
List all sequence authors (use the Add button for more than one)
Reference Information #1:
Select publication status (unpublished, in-press, or Published)
    - If in-press add reference title, journal title, year, volume, issue, and page numbers
    - If published add reference title, journal title, year, volume, issue, page numbers, and PubMed ID
    - Optional: if unpublished add reference title
Select reference authors as "Same as Sequence Authors" or "Specify New Authors"
    - If specify new authors, list authors
(Optional) Add Another Reference:
Follow Reference Information #1 steps
SECTION: Submitting to Bankit
5. Sequencing Technology:
Select the sequencing technology (or other and specify)
Select unassembled sequence reads or assembled sequences (consisting of two or more sequence reads)
List assembly program and version or date

Example: Illumina, Geneious v. Geneious Prime 2023.0.1
SECTION: Submitting to Bankit
6. Submission Release Date:
Select "Immediately after processing" or "Release date" 
    - If Release Date is selected, specify date in DD-Mon-YYYY format
Sequence(s) and Definition Line(s):
Choose molecule type, linear or circular, if it is a complete sequence, and fasta or alignment format
Either download sequence file or copy and paste it in the box
    - Note: make sure the first line follows this format; make everything in bold specific to your submission
            >Seq#[organism=genus species] species straininfo

Example: >Seq1[organism=Enterovirus rhinovirus] Rhinovirus C17 strain RvC17/USA/2019
SECTION: Submitting to Bankit
7. Submission Category:
Select "Original" or "Third Party Annotation"
SECTION: Submitting to Bankit
8. Source Modifiers:
Choose organelle/location if applicable
Choose source modifiers and list information in value column, add as many as desired
 
Example: Strain = RvC17/USA/2019, host = homo sapiens, tissue_type = Lung, country = USA, collection_date = 2019
SECTION: Submitting to Bankit
9. Features (Overview):
Select "Add features by completing input forms"
Select "Coding Region (CDS) / Gene / mRNA"
Select "providing intervals"
Click Add
SECTION: Submitting to Bankit
10. Features (Detail): 
Choose if the CDS is on the + or - strand
If the CDS is not compete, select 5' or 3' for which end it is incomplete at
Select "Entire Sequence" or "Specific Spans" for Nucleotide Interval Spans
    - If Specific Spans, specify start and stop and which strand it is on
List protein name (optional: also list protein description and EC number)
Click accept

Example:  specific spans: start = 19 stop = 6498 strand = -minus; protein name = polyprotein
SECTION: Submitting to Bankit
11. Review Submission:
Make sure everything looks good
If resubmitting check the box under the resubmission section