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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load bwa
# Index fasta file
bwa index ref.fa
# Align Illumina/454/IonTorrent single-end reads
# longer than ~70bp
bwa mem -t ${NSLOTS} \
ref.fa reads.fq > aln.sam