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!
tutorial/intro tutorial/setup tutorial/example-data tutorial/custom-data tutorial/genomic-surveillance tutorial/next-steps tutorial/videos
visualization/sharing visualization/interpretation visualization/narratives
guides/update-workflow guides/data-prep/index guides/workflow-config-file guides/customizing-visualization guides/run-analysis-on-terra
reference/nextstrain-overview reference/files reference/workflow-config-file reference/remote_inputs reference/metadata-fields reference/naming_clades reference/data_submitter_faq reference/troubleshoot reference/change_log reference/glossary
Stuck? Ask us on the discussion board. We're happy to help! <https://discussion.nextstrain.org/>