About

This repository analyzes viral genomes from Washington State using Nextstrain. This is a copy of the original Nextstrain ncov repository that has been modified for Washington-specific builds. These modifications draw heavily from work by John Huddleston in the SPHERES augur build.

Usage

Clone this repository.

git clone https://github.com/blab/ncov-wa-build.git
cd ncov-wa-build/

Modify build definitions, as needed, in wa_profile/wa/builds.yaml.

If running externally

Download sequences from GISAID. You will require a GISAID login to do so.

1. Log into GISAID's EpiCoV site
2. Click "Downloads" to bring up a modal window
3. In this window click on "nextmeta" to download the file nextstrain_metadata.tsv.bz2. This should be decompressed and saved as data/metadata.tsv.
4. Then, in this window click on "FASTA" to download the file nextstrain_sequences.fasta.bz2. This should be decompressed and saved as data/sequences.fasta. For more details, see "Contextualizing your data" at this guide.

Run the workflow:

snakemake --profile wa_profiles/wa-external/

If Nextstrain team member

If running on Fred Hutch rhino cluster:

snakemake --profile wa_profiles/wa-rhino/

If running on aws-batch:

snakemake --profile wa_profiles/wa/