Introduction

BWA (Burrows-Wheeler Aligner)is a program that aligns short deep-sequencing reads to long reference sequences. Here is a short tutorial on the installation and steps needed to perform alignments. You can align the short reads to the genome or the transcriptome depending on the experiment/application.

Installation

Download and install BWA on a Linux/Mac machine

NOTE: You need to do this only once!!

Download: http://sourceforge.net/projects/bio-bwa/files/

Download  bwa-0.7.17.tar.bz2

Then:

bunzip2 bwa-0.7.17.tar.bz2

tar xvf bwa-0.7.17.tar

cd bwa-0.7.17

make

Add bwa to your PATH by editing ~/.bashrc and adding

export PATH=$PATH:/path/to/bwa-0.5.9    # /path/to is an example ! replace with real path on your machine

Then execute the command in using source.

source ~/.bashrc

(in some systems, ~/.bash_profile is used in place of ~/.bashrc)

Then, to test if the installation was successful, just type:

bwa

If Unix can find bwa, the 'bwa' command alone will show you all of the options available.

source  : Elementolab/BWA tutorial