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.

If you prefer video format to working through this tutorial in the written documentation, check out the video tutorial walkthrough.

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!