A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2

This is the documentation for the SARS-CoV-2 workflow maintained and actively used by the Nextstrain core team.

In addition to the phylogenetic analysis described here, you can use Nextclade our “drag-and-drop” tool for clade assignment, mutation calling, and sequence quality control at clades.nextstrain.org.

If something in this documentation is broken or unclear, open an issue so we can improve it for everyone.

If you have a specific question, post a note on the discussion board – we’re happy to help!