SARS-CoV-2_Analysis

A Snakemake workflow for large-scale SARS-CoV-2 analyses.

Usage

First, clone the repository:

git clone https://github.com/cbg-ethz/SARS-CoV-2_Analysis

If needed, search for new samples using QuerySRAAccessions.ipynb.

The whole analysis can then be reproduced by executing the following line:

./run_pipeline.sh

This will download the reads, compute coverages, call variants, and plot summary figures.