Abismal

Introduction

Another Bisulfite Mapping Algorithm (abismal) is a read mapping program for bisulfite sequencing in DNA methylation studies.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/abismal
Home page: https://github.com/smithlabcode/abismal

Versions

  • 3.0.0

Commands

  • abismal

  • abismalidx

  • simreads

Module

You can load the modules by:

module load biocontainers
module load abismal

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 abismal on our clusters:

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

module --force purge
ml biocontainers abismal

abismalidx  ~/.local/share/genomes/hg38/hg38.fa hg38