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GenomeSharing
Currently the vast majority (>90%) of SARS-CoV-2 genomes are shared via GISAID. This platform was built to encourage the sharing of influenza genomes, and in this regard appears to have been successful. It uses a data usage agreement (DUA) and to allow researchers to share with the platform, and the platform to share with other researchers who have agreed to the DUA. Unfortunately, this requires manual curation of registrants, and prevents the development of derivative, open data products using the genomes in GISAID.
We will support the development of an open submission process that GISAID users can transition to with no more effort than email verification and confirmation of the transfer. Our approach will be to provide a portal that simplifies the submission of existing GISAID entries to GenBank. We will collect metedata from GISAID and store it in a repository operated by members of the group who have signed the GISAID DUA. GISAID submitters will be encouraged to use this simple interface to rapidly co-submit their SARS-CoV-2 genomes to GenBank.
We will consider the possibility of a consortium paper based on the GISAID SARS-CoV-2 genomes. Our aim will be a short paper that describes the features of the SARS-CoV-2 pangenome. GISAID contributors will be encouraged to participate in this paper, and to release their data to GenBank as part of this process. This will mitigate concerns about credit which have fostered the development of the DUA model in GISAID.
- Build web application providing a "one-click" style interface to submit genomes already in GISAID to GenBank, provided the user can verify their identity via email.
- Encourage GISAID submitters to verify with the application and allow us to submit their SARS-CoV-2 genomes (with metadata and attribution) to GenBank.
- Explore the possibility of a pangenome model built from SARS-CoV-2 and publication of the same.
- Erik Garrison (UCSC, based in Italy, @erikgarrison, GitHub: ekg)
- Konrad Förstner (ZB MED, Twitter: @konradfoerstner, GitHub: konrad)