TITLE: Overview of NCBI&#39;s SARS-CoV-2 submission process and the metadata required
AUTHORS: Ruth E Timme, Emma Griffiths, Lee Katz

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span></div><div class = "text-block"><span style = "font-weight:bold;">This protocol explains the metadata requirements for the following two protocols:</span></div><div class = "text-block"><span style = "font-weight:bold;">Complete in order (1 then 2):</span></div><div class = "text-block"><span style = "font-weight:bold;">1. </span><a href="https://www.protocols.io/edit/sars-cov-2-ncbi-submission-protocol-sra-biosample-br8ym9xw" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject</span></a></div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">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.</li><li style = "counter-reset:ol0;list-style-type:disc;">SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample.</li><li style = "counter-reset:ol0;list-style-type:disc;"></li><li style = "counter-reset:ol0;list-style-type:disc;"><span style = "font-weight:bold;">2. </span><a href="https://www.protocols.io/edit/sars-cov-2-ncbi-consensus-submission-protocol-genb-bid7ka9n" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SARS-CoV-2 NCBI consensus submission protocol: GenBank</span></a></li><li style = "counter-reset:ol0;list-style-type:disc;"><span>     </span><span style = "font-style:italic;">Required</span><span>: established BioProject and BioSamples</span></li><li style = "counter-reset:ol0;list-style-type:disc;">Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data.</li></ul></div><div class = "text-block"><span style = "font-weight:bold;">2. </span><a href="https://www.protocols.io/edit/sars-cov-2-ncbi-consensus-submission-protocol-genb-bid7ka9n" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SARS-CoV-2 NCBI consensus submission protocol: GenBank</span></a></div><div class = "text-block"><span>     </span><span style = "font-style:italic;">Required</span><span>: established BioProject and BioSamples</span></div><div class = "text-block"><ul style = "list-style-type:disc;"></ul></div></div>

[STEPS]
?. [Three templates needed for NCBI SARS-CoV-2 submission]
START HERE FIRST:  Read the PHA4GE contextual data specification BEFORE populating your submission templates!
?. [Three templates needed for NCBI SARS-CoV-2 submission]
Training video:For the visual learners, here is a 10min video summarizing the entire NCBI submission process:
?. [Three templates needed for NCBI SARS-CoV-2 submission]
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 templateStep 3) PHA4GE SRA metadata templateStep 4) PHA4GE GenBank source modifier templateStep 3) PHA4GE SRA metadata templateStep 4) PHA4GE GenBank source modifier template
?. [BioSample metadata]
SARS-CoV-2 BioSample submission package:Download custom version containing the PHA4GE pick-lists and controlled vocabulary:Follow the PHA4GE contextual metadata SOP and guidance posted at NCBI for populating the template.
?. [SRA metadata]
Populate SRA’s batch metadata table:Download File:Follow guidance presented in this file for 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.
?. [GenBank metadata]
Populate GenBank source modifier template:Download file:Follow guidance presented in this file for populating the template.