Prototype of state- and territory-level SARS-CoV-2 Nextstrain builds for the United States. Note: Do not use these to make any scientific conclusions!
Choose a top-level working directory for your analyses. Clone the Nextstrain ncov repository into that top-level directory.
git clone https://github.com/nextstrain/ncov.gitClone this repository into the same top-level directory.
git clone https://github.com/huddlej/usa-sarscov2.gitChange into the ncov directory.
cd ncov/Run the workflow on a SLURM cluster.
snakemake --profile ../usa-sarscov2/profiles/usa/View the resulting builds with auspice from a local machine.
auspice view