Module 3.5 – Public genome repositories for SARS-CoV-2

What to know

This module introduces two public repositories for sharing SARS-CoV-2 genome sequence data—Global Initiative on Sharing All Influenza Data (GISAID) and the National Center for Biotechnology Information (NCBI)—and provides basic tips for searching them.

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Overview

Presenter: Michael Weigand, PhD | Bioinformatician, CDC
Download Presentation Slides [PDF - 21 slides]


Further Reading

  1. Global Initiative on Sharing All Influenza Data (GISAID).
  2. National Center for Biotechnology Information (NCBI) SARS-CoV-2 resources.
  3. NCBI Virus SARS-CoV-2 data dashboard.
  4. NCBI Umbrella BioProject of US sequencing efforts.
  5. NCBI GenBank submission.
  6. NCBI SRA submission.
  7. Public Health Alliance for Genomic Epidemiology (PHA4GE) resources.
  8. Public Health Alliance for Genomic Epidemiology (PHA4GE) protocols.
  9. SARS-CoV-2 GISAID submission protocol.
  10. SARS-CoV-2 GenBank submission protocol.
  11. SARS-CoV-2 SRA submission protocol.

Additional Resources

  1. Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group. Austin, et al. Wellcome Open Research, updated 2021.
  2. Shortcomings of SARS-CoV-2 genomic metadata. Gozashti and Corbett-Detig. BMC Res Notes, 2021.
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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)