BWA

Overview

BWA (Burrow-Wheeler Aligner) is a software package for mapping DNA 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 a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Using

Use the module name bwa to discover versions available and to load the application.

Multicore

The bwa application allows you to define multiple cores/threads. For more details look at the specific bwa command for further details, for example bwa mem to read about the -t option.