# bwa

## Summary

+ **Module Name:** bwa
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://bio-bwa.sourceforge.net/](http://bio-bwa.sourceforge.net/)

## Software Description

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.
## General Linux

To run this software interactively in a Linux environment run the commands:

	module load bwa
	bwa

For each of the BWA algorithms, you must first index the genome with the following command:

	bwa index [options] input.fasta

BWA programs may also be submitted to a queue using Slurm script such as the one below:

	#!/bin/bash
	#SBATCH --nodes=1 --ntasks-per-node=16
	#SBATCH --mem-per-cpu=1000M
	#SBATCH --time=8:00:00
	#SBATCH --mail-type=ALL
	#SBATCH --mail-user=sample_email@umn.edu

	module load bwa
	bwa index input.fasta
	bwa aln -t $SLURM_NTASKS input.fasta input.fq > output.sai

Note the use of -t $SLURM_NTASKS; this option is used to specify the number of threads used by BWA.

A list of options is available at the BWA manual page.

To run the BWA-backtrack alignment algorithm, use any of the following commands:

	bwa aln
	bwa samse
	bwa sampe

The BWA-SW algorithm can be run using

	bwa bwasw

The BWA-MEM algorithm can be run using

	bwa mem

## Slurm Example


	#!/bin/bash
	#SBATCH --job-name="rfm_RunBWATest_job"
	#SBATCH --ntasks=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --output=rfm_RunBWATest_job.out
	#SBATCH --error=rfm_RunBWATest_job.err
	#SBATCH --time=0:10:0
	#SBATCH -p msismall
	module load bwa/0.7.17
	wget https://public.s3.msi.umn.edu/reframe/sw/bwa/sample.fq
	wget https://public.s3.msi.umn.edu/reframe/sw/bwa/ref.fasta
	bwa index ref.fasta
	bwa aln -t 4 ref.fasta sample.fq > output.sai