Sourmash

Introduction

Sourmash is a tool for quickly search, compare, and analyze genomic and metagenomic data sets.

For more information, please check its website: https://biocontainers.pro/tools/sourmash and its home page on Github.

Versions

• 4.3.0

• 4.5.0

Commands

• sourmash

Module

You can load the modules by:

module load biocontainers
module load sourmash

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Sourmash on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sourmash
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers sourmash

sourmash sketch dna -p k=31 *.fna.gz
sourmash compare *.sig -o cmp.dist
sourmash plot cmp.dist --labels