TITLE: SARS-CoV-2 NCBI submission workflow + guidance for structuring and releasing metadata
AUTHORS: Ruth Timme, Emma Griffiths

[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 workflow provides an overview on the metadata specification recommend for SARS-CoV-2 sequence data and a series of protocols outlining the steps for NCBI submission.</span></div><div class = "text-block"><a href="https://dx.doi.org/10.17504/protocols.io.btpznmp6" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">PHA4GE Contextual Metadata SOP:</span></a></div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">This protocol provides step-by-step instructions for populating the template, and also addresses a number of ethical, privacy and practical considerations that should be discussed with your data steward prior to any type of data sharing.</li><li style = "counter-reset:ol0;list-style-type:disc;">The appendices provide additional instructions and examples of how to curate sample type descriptions, and how to identify additional standardized terms should you need them.</li><li style = "counter-reset:ol0;list-style-type:disc;"></li><li style = "counter-reset:ol0;list-style-type:disc;"><a href="http://dx.doi.org/10.17504/protocols.io.bsbpnamn" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">Overview of NCBI's submission process and the metadata required:</span></a></li><li style = "counter-reset:ol0;list-style-type:disc;">Provides an overview of the submission process and includes a brief training video.</li><li style = "counter-reset:ol0;list-style-type:disc;"></li><li style = "counter-reset:ol0;list-style-type:disc;"><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></li><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;"><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"><a href="http://dx.doi.org/10.17504/protocols.io.bsbpnamn" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">Overview of NCBI's submission process and the metadata required:</span></a></div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Provides an overview of the submission process and includes a brief training video.</li><li style = "counter-reset:ol0;list-style-type:disc;"></li><li style = "counter-reset:ol0;list-style-type:disc;"><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></li><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;"><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"><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;"><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"><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]