Burrows-Wheeler Aligner

Introduction

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. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Installed version

The currently installed version of BWA is 0.7.12.

Using BWA

If you want to find out more about BWA on the HPC cluster, you can use the command

module spider bwa.kit

This will show you basic informations e.g. a short description and the currently installed version.

To load the module, use the command

module load bwa.kit

There is only one version of BWA installed at the moment, if there should be more than one you would have to specify the right version to load:

module load bwa.kit/0.7.12

Always remember: this command is case sensitive!

Using BWA with the HPC cluster

If you want to use BWA on the HPC cluster, you will have to create a jobscript which is than processed by SLURM.

An example jobscript could look like this:

#!/bin/bash 

#SBATCH --ntasks=1
#SBATCH --mem=2G
#SBATCH --time=0-2:00  
#SBATCH --job-name=BWA-TEST
#SBATCH --output=bwa-test.%j.out        
#SBATCH --error=bwa-test.%j.err   

##YOUR SCRIPT STARTS HERE
bwa ..

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

Documentation

For further informations, please visit the official manual.