Burrows-Wheeler Aligner, a genomic sequence mapping program
BWA, which is an acronym for the Burrows-Wheeler Aligner, is a genomic sequence mapping program which is designed to map low-divergent sequence reads against large reference genomes using one of three algorithms:
- BWA-backtrack, which is intended for use with Illumina sequence reads of up to 100 base pairs;
- BWA-MEM which is meant for longer sequence reads of 70 base pairs up to 1Mbp and supports long-reads and split alignment
- BWA-SW, which is similar to BWA-MEM.
In general, BWA-MEM is the latest algorithm and the one recommended for high-quality queries due to it being faster and more accurate.
Using BWA on the HPC#
The following shows an example of using BWA on the HPC.
From an HPC login node, run the following commands:
For a complete set of commands, refer to the BWA Manual.