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

This template and tutorial will walk you through the process of running a basic phylogenetic analysis on SARS-CoV-2 data. We’ve created these resources with the goal of enabling Departments of Public Health to start using Nextstrain to understand their SARS-CoV-2 genomic data within 1-2 hours. In addition to the phylogenetic analysis described here, you can use our “drag-and-drop” tool for a clade assignment, mutations calling, and basic sequence quality checks at clades.nextstrain.org.

We also recommend this 1-hour video overview by Heather Blankenship on how to deploy Nextstrain for a Public Health lab.

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

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