Burrows-Wheeler Aligner (BWA)

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 100bps, while SW/MEM are designed for reads ranging from 70 - 1Mbp. It accepts a reference genome and a FASTQ file and outputs to a SAM file.

For additional information see the documentation

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

Parallel Capabilities: Single core default, Multithreading options supported.