2023-clean-gtdb

An experimental snakemake workflow repository to remove suppressed or replaced genomes from sourmash workflow.

Introduction

This workflow uses sourmash's manifest and picklist to exclude supressed and replaced genomes from the prepared GTDB database of sourmash.

Operation

To install this workflow:

git clone https://github.com/dib-lab/2023-clean-gtdb.git

or

git clone git@github.com:dib-lab/2023-clean-gtdb.git

cd 2023-clean-gtdb
conda env create --name clean-db --file environment.yml
conda activate clean-db

To run this workflow:

snakemake -s clean-gtdb.snakefile --use-conda --rerun-incomplete -j 1

or

snakemake -s clean-gtdb.snakefile -j 3 --use-conda --rerun-incomplete --resources mem_mb=12000 --cluster "sbatch -t {resources.time_min} -J clean-gtdb -p bmm -n 1 -N 1 -c {threads} --mem={resources.mem_mb}" -k

Visualizations