Mashmap

Introduction

Mashmap is a fast approximate aligner for long DNA sequences.

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

Versions

• 2.0-pl5321

Commands

• mashmap

Module

You can load the modules by:

module load biocontainers
module load mashmap

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 Mashmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=mashmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mashmap

mashmap -r ref.fasta -t 12 -q input.fasta