View source for 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 versions of BWA are 

On environment ''hpc-uniol-env'':
 '''bwa.kit/0.7.12'''
On environment ''hpc-env/6.4'':
 '''BWA/0.7.17-intel-2018a'''
On environment ''hpc-env/8.3'':
 '''BWA/0.7.17-GCC-8.3.0'''
 '''BWA/0.7.17-GCCcore-8.3.0'''

== 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.

Depending on the environment you work on or the version you need, you have either to load

 module load bwa.kit

or you have to change to the new  environment at first:

 module load hpc-env/6.4
 module load BWA

Always remember: this commands are 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 Job Management (Queueing) System|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 ..

You can find a short manual on how to use BWA [http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial#Download_the_reference_genome here].

Additionally, you can get a quick overview of the available commands, by just typing ''bwa'' into the console after loading the module. You will then get a short summary of the commands for ''bwa'.
The new version 0.7.17, which is installed on the environment ''hpc-env/6.4'' does additionally come with a   man page.
To read it, you have to type in
 man bwa
== Documentation ==

For further informations, please visit the [http://bio-bwa.sourceforge.net/bwa.shtml official manual].