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URL: https://dx.doi.org/DOI:10.17504/protocols.io.bf7bjrin

Authors: Ruth Timme, Emma Griffiths, Heather Blankenship, Erin Young, Duncan MacCannell, Stacia Wyman

Group: GenomeTrakr, Coronavirus Method Development Community, PHA4GE

Summary: PURPOSE: This is a SARS-CoV-2 specific protocol that covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. These protocols cover submission using NCBI's Submission Portal web-interface.Complete in order (1 then 2):1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject (included protocol)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.2. SARS-CoV-2 NCBI assembly submission protocol: GenBank Required: established BioProject and BioSamplesSubmit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data.2. SARS-CoV-2 NCBI assembly submission protocol: GenBank Required: established BioProject and BioSamples

Affiliations: US Food and Drug Administration, University of British Columbia, Michigan Department of Health and Human Services, Utah Public Health Laboratoraty, Centers for Disease Control and Prevention, Innovative Genomics Institute, UC Berkeley

Version: 1

Publication Date: 2020

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