TITLE: SARS-CoV-2 ENA submission workflow + guidance for structuring and releasing metadata
AUTHORS: Nabil-Fareed Alikhan, Ruth E Timme, Emma Griffiths, 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 recommended for SARS-CoV-2 sequence data and a series of protocols outlining the steps for ENA 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="https://www.protocols.io/view/sop-for-populating-ebi-submission-templates-ena-bh5dj826" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SOP for populating EBI submission templates (ENA)</span></a></li><li style = "counter-reset:ol0;list-style-type:disc;">Guidance for populating the ENA metadata template using PHA4GE fields and terms.</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/view/sars-cov-2-ebi-submission-protocol-ena-biosample-a-bhwdj7a6" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SARS-CoV-2 EBI submission protocol: ENA, BioSample, and BioProject</span></a></li><li style = "counter-reset:ol0;list-style-type:disc;">Step-by-step instructions for establishing a new EBI (Webin) 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 ENA (European Nucleotide Archive) and metadata to BioSample.</li></ul></div><div class = "text-block"><a href="https://www.protocols.io/view/sop-for-populating-ebi-submission-templates-ena-bh5dj826" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SOP for populating EBI submission templates (ENA)</span></a></div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Guidance for populating the ENA metadata template using PHA4GE fields and terms.</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/view/sars-cov-2-ebi-submission-protocol-ena-biosample-a-bhwdj7a6" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SARS-CoV-2 EBI submission protocol: ENA, BioSample, and BioProject</span></a></li><li style = "counter-reset:ol0;list-style-type:disc;">Step-by-step instructions for establishing a new EBI (Webin) 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 ENA (European Nucleotide Archive) and metadata to BioSample.</li></ul></div><div class = "text-block"><a href="https://www.protocols.io/view/sars-cov-2-ebi-submission-protocol-ena-biosample-a-bhwdj7a6" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">SARS-CoV-2 EBI submission protocol: ENA, 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 EBI (Webin) 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 ENA (European Nucleotide Archive) and metadata to BioSample.</li></ul></div></div>

[STEPS]