TITLE: Overview of NCBI&#39;s SARS-CoV-2 submission process and the metadata required
AUTHORS: Ruth  Timme, Emma  Griffiths, Lee  Katz, Michael  Weigand, Technical  Outreach and Assistance for States Team

[DESCRIPTION]
PURPOSE: 
This protocol explains the metadata requirements for the following two protocols:

1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject 
Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort.
SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample.  Users can modify this protocol to just create a BioSample with no linked raw data. 

2. SARS-CoV-2 NCBI consensus submission protocol: GenBank
     Required: established BioProject and BioSamples
Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data.

Version history:
V5: Updated metadata templates (BioSample) for minor edit

[STEPS]
SECTION: Three templates needed for NCBI SARS-CoV-2 submission
1. START HERE FIRST:  Read the PHA4GE contextual data specification BEFORE populating your submission templates!

Direct link to the PHA4GE GitHub repository: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/tree/version_3_dev
SECTION: Three templates needed for NCBI SARS-CoV-2 submission
1.1. Training video:

For the visual learners, here is a 10min video summarizing the entire NCBI submission process:
 

SECTION: Three templates needed for NCBI SARS-CoV-2 submission
1.2. Assembling the three NCBI metadata templates for SARS-CoV-2 submission:

Steps 2-4 provide templates to populate for your submission, however, the primary PHA4GE guidance should be followed first to ensure the correct controlled vocabularies and ontology terms are used to populate these fields. 

Guidance included in this protocol:  
Step 2) PHA4GE BioSample metadata template

Step 3) PHA4GE SRA metadata template

Step 4) PHA4GE GenBank source modifier template

  
SECTION: BioSample metadata
2. SARS-CoV-2 BioSample submission package:

Download custom version containing the PHA4GE pick-lists and controlled vocabulary:

  

Follow the PHA4GE contextual metadata SOP and source GitHub repository for guidance in populating the template.

SECTION: SRA metadata
3. Populate SRA’s batch metadata table:

Download custom version containing the PHA4GE pick-lists and controlled vocabulary:

 

Follow the PHA4GE contextual metadata SOP and source GitHub repository for guidance in populating the template.

PRO TIPS:
If you have sequences to submit that belong to more than one BioProject, create a separate submission + metadata table for each of your BioProjects. 
Entering fastq filenames in the spreadsheet: On a Mac, you can directly copy the file names from the folder into a spreadsheet. This is not possible on a PC using copy and paste but can be done with some command-line operation. 
Finally, it is important to develop a QA/QC step to make sure the files are associated with the correct sample name. For example, use a left function in excel to strip of the appended text in the file name and then use the exact match to make sure the name matches the sample name.
SECTION: GenBank metadata
4. Populate two GenBank templates. 

1. GenBank structured comment (metadata describing the mapping or assembly methods)

  

2. GenBank source modifier template. This is a custom version containing PHA4GE guidance and direct linkage to the respective BioSample records. Follow guidance presented in this file for populating the template.