sars-covid-2-ncbi

Download sars-covid-2 sequencing runs from NCBI

Run accessions and metadata was downloaded from https://trace.ncbi.nlm.nih.gov. Runs were filtered by AssayType=="rna-seq" and Platform=="ILLUMINA".

Install workflow

• Install Snakemake as described in https://github.com/avilab/sarscov2.

• Create a new working directory e.g. covid2-ncbi and (Fork +) clone this repository to working directory.

mkdir covid2-ncbi
cd covid2-ncbi
git clone https://github.com/avilab/sars-covid-2-ncbi.git .

Running

Test run:

snakemake --use-conda -n

Download sequencing runs listed in SraRunTable.txt, e.g. in slurm cluster:

snakemake --use-conda --cluster "sbatch -p main --mem 2000 -t 60" -j

For all possible snakemake command line options please refer to snakemake tutorial https://snakemake.readthedocs.io/en/stable/executing/cli.html.