Burrows-Wheeler Aligner

Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

BWA ia available as a module on Apocrita.

Usage

To run the default installed version of BWA, simply load the bwa module:

$ module load bwa
$ bwa

Usage:   bwa <command> [options]

For full usage documentation, run bwa without a command.

Example job

Serial job

Here is an example job running on 1 core and 2GB of memory:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=2G   # Request 2GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load bwa

# Index fasta file
bwa index ref.fa

# Align Illumina/454/IonTorrent single-end reads
# longer than ~70bp
bwa mem -t ${SLURM_NTASKS} \
        ref.fa reads.fq > aln.sam

References

• BWA GitHub
• BWA manual