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Tutorial: Using Nextstrain for SARS-CoV-2


1. Setup and installation
2. Preparing your data
3. Orientation: analysis workflow
4. Orientation: files
5. Running & troubleshooting
6. Customizing your analysis
7. Customizing your visualization

Visualization & interpretation

8. Options: visualizing and sharing
9. Interpreting your results
10. Writing a narrative

Stuck? Ask us on the discussion board. We're happy to help!

This project is maintained by nextstrain

Nextstrain Narratives

Nextstrain Narratives allow you to pair a specific view of a dataset with text and images to generate scrollable, interactive reports.

For examples, see our weekly Situation Reports from the first several months of the pandemic.

You can read more about Narratives here. We've also provided a template narrative file for you to edit.
You can preview the template narrative by navigating to

We'll add more to this page soon; in the meantime, if you get stuck, don't hesitate to ask for help! :)

Previous Section: Interpreting your results