Template repository for SARS-CoV-2 analyses

This repository is a template and tutorial for 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.

If you're looking for the SARS-CoV-2 analyses used for the main Nextstrain builds, please see this repository instead.

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 also just use our example data to start.

1. Preparing your data
2. Set up and installation
3. Orientation: analysis workflow
4. Orientation: which files should I touch?
5. Running & troubleshooting
6. Customizing your analysis
7. Customizing your visualization

Getting started with visualization & interpretation

The starting point for this section is a JSON file. You can also just use our examples to start.

8. Options for visualizing and sharing results
9. Interpreting your results
10. Writing a narrative to highlight key findings
11. Case studies: interpreting your data (coming soon!)

Quickstart

If you'd prefer, you can also start by running a basic analysis on the provided example data and/or visualizing the output with the auspice.us drag-and-drop viewer. If you get stuck at any point, you can find more detailed instructions in the full tutorial outlined above.

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

1. Clone this repository

git clone https://github.com/nextstrain/sarscov2-tutorial.git

2. Install augur for bioinformatics

python3 -m pip install nextstrain-augur

MacOS:

brew install mafft iqtree raxml fasttree vcftools

Ubuntu/Debian:

sudo apt install mafft iqtree raxml fasttree vcftools

3. Run basic analysis on example data

sarscov-tutorial$ snakemake --profile ./my-analyses/example

4. Visualize your results (or our example output)

Go to https://auspice.us in your browser. Drag and drop ./auspice/sarscov2.json (or any other JSON in this directory) anywhere on the screen.

Voila!

Help

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!