Burrows-Wheeler Aligner (BWA)

Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome. It consists of 3 algorithms: BWA-backtrack, BWA-SW, and BWA_MEM. Backtrack is designed for Illumina sequence reads up to 100 bps, while SW/MEM are designed for reads ranging from 70 - 1 Mbps. It accepts a reference genome and a FASTQ file and outputs to a SAM file.

For additional information, see the BWA documentation.

ml biocontainers bwa
bwa aln <reference> <short seq.fq> > <output.sam>

Parallel Capabilities: Single core default, multithreading options supported.