BWA

Overview

Burrows-Wheeler Alignment Tool 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.

Usage

Check availability and versions of BWA installed:

$ module avail bwa

We recommend using the latest version. Always load a module for specific version. Example:

$ module load bwa/0.7.17

Loading a module adds location of binaries, libraries, include files, manpages, etc. to respective environment variables PATH, LIBRARY_PATH, LD_LIBRARY_PATH, MANPATH, etc. For more details see modules help guide.

To run BWA do something like

$ bwa index ref.fa

Useful Links

For documentation look at http://bio-bwa.sourceforge.net/bwa.shtml