BWA

Introduction

BWA (Burrows-Wheeler Aligner) is a fast, accurate, memory-efficient aligner for short and long sequencing reads.

For more information, please check its website: https://biocontainers.pro/tools/bwa and its home page: http://bio-bwa.sourceforge.net.

Versions

  • 0.7.17

Commands

  • bwa

  • qualfa2fq.pl

  • xa2multi.pl

Module

You can load the modules by:

module load biocontainers
module load bwa

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 BWA on our clusters:

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

module --force purge
ml biocontainers bwa

bwa index ref.fasta
bwa mem ref.fasta input.fq > test.sam