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.


BWA 0.7.17 can be activated using the module file:

module load apps/bwa/0.7.17/gcc-6.2

The BWA executable is bwa. Type bwa for a list of commands.

Installation notes

BWA 0.7.17 was installed using the script; the module file is /usr/local/modulefiles/apps/bwa/0.7.17/gcc-6.2. The installation of BWA 0.7.17 was compiled with GCC 6.2.0.