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.
Overview: complete walkthrough
Getting started with analysis
The starting point for this section is a FASTA file with sequence data + a TSV file with metadata. You can alternately use our example data to start.
- Setup and installation
- Preparing your data
- Orientation: analysis workflow
- Orientation: which files should I touch?
- Running & troubleshooting
- Customizing your analysis
- Customizing your visualization
Getting started with visualization & interpretation
The starting point for this section is a JSON file. You can alternately use our examples to start.
- Options for visualizing and sharing results
- Interpreting your results
- Writing a narrative to highlight key findings
- Case studies: interpreting your data (coming soon!)
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!