BWA BWA stands for Burrows-Wheeler Aligner. BWA is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

On the 24 GB memory nodes load BWA by typing the following:

$ module load gcc bwa 

On the high memory nodes BWA is at /usr/bin/bwa installed from Ubuntu.

Here is an example submit script.

#!/bin/bash
#$ -cwd
### Job name:
#$ -N MyJobName
#$ -S /bin/bash
$ module load gcc bwa

bwa index -a bwtsw tttF3.csfasta
bwa aln tttF3.csfasta ttt.fastq > ttt.sai
bwa samse tttF3.csfasta ttt.sai ttt.fastq > ttt.sam

BWA Manual