Ismapper

Introduction

ISMapper searches for IS positions in sequence data using paired end Illumina short reads, an IS query/queries of interest and a reference genome. ISMapper reports the IS positions it has found in each isolate, relative to the provided reference genome.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/ismapper

Home page: https://github.com/jhawkey/IS_mapper

Versions

• 2.0.2

Commands

• ismap

Module

You can load the modules by:

module load biocontainers
module load ismapper

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 ismapper on our clusters:

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

module --force purge
ml biocontainers ismapper