NCBI submission protocol for microbial pathogen surveillance v2

PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and to the NCBI Pathogen Detection portal. This protocol 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. SCOPE: for use by any laboratory submitting WGS data for bacterial pathogens, including pathogens under surveillance at NCBI Pathogen Detection. (This includes US laboratories in GenomeTrakr, NARMS, Vet-LIRN, PulseNet, and other non-US networks and submitters). 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 to get your NCBI submission environment established, then contact gb-admin@ncbi.nlm.nih.gov to set up an account for submitting through the API. This protocol covers submissions using NCBI's Submission Portal web-interface. Version history: V9: Updated external protocol links and modified Step 2.5 to reflect the option to choose the most appropriate metadata package. V8: Corrected the multi-species umbrella project accession in Step 1.5 V7: Updated guidance for creating new BioProjects, including projects for non-targeted species V6: minor edits including updating links out to other protocols. V5: Linking directly to the metadata template guidance instead of including duplicate copies of the files in this protocol. Updated screenshot for choosing the pathogen template to reflect changes at NCBI. V4: updated screenshots to reflect NCBI submission portal changes. Updated custom BioSample template.