Software: ISMapper
Description
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.
Available Versions
| Unspecified: | 2.0.2 |
|---|
BioContainers: https://biocontainers.pro/tools/ismapper
Home page: https://github.com/jhawkey/IS_mapper
Commands
- ismap
Module
You can load the modules by:
module load biocontainers
module load ismapper
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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