SPHERES augur builds

About

This repository analyzes viral genomes using Nextstrain to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, evolves and spreads. This is a copy of the original Nextstrain ncov repository.

Usage

Clone this repository.

git clone https://github.com/nextstrain/spheres-augur-build.git
cd spheres-augur-build/

Modify build definitions, as needed, in spheres_profile/builds.yaml. For more details about modifying builds, see the SPHERES profile README. Run the workflow.

snakemake --profile spheres_profile/

View the resulting builds with auspice from a local machine.

auspice view