Mash

Mash is a fast tool for estimating the distance between genomes and metagenomes using the MinHash dimensionality-reduction technique. It reduces large sequences to compact sketches, enabling rapid distance and containment estimates.

Mash

License

Free to use and open source. See the Mash license.

Available

Roihu: 2.3, via the bio-apps module.

Usage

Mash is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Mash module:

module load bio-apps/v202603
module load mash/2.3

Create sketches and estimate the distance between two genomes:

mash sketch -o reference genome1.fa
mash dist reference.msh genome2.fa

Example batch script

#!/bin/bash
#SBATCH --job-name=mash
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load mash/2.3

mash sketch -p $SLURM_CPUS_PER_TASK -o reference *.fa

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk