BWA

Burrows-Wheeler Aligner (BWA) is an open-source software package for mapping DNA sequencing reads to a reference genome. It was developed by Heng Li and colleagues at the Broad Institute and first released in the late 2000s. BWA uses the Burrows-Wheeler transform and FM-index to achieve fast, memory-efficient alignment of short reads across large genomes.

The software offers two main algorithmic flavors. BWA-backtrack (including bwa aln and bwa samse/sampe) was the original approach and remains useful for certain error profiles. A more widely used component is BWA-MEM, introduced later, which employs a seed-and-extend strategy and is optimized for longer reads and higher accuracy. BWA supports single-end and paired-end reads, various read lengths, and gapped alignment. It indexes the reference genome with bwa index and produces alignments in SAM format (often converted to BAM for storage). It also reports mapping quality scores and supports read group information for downstream analyses. The tool is multithreaded and designed to operate on standard workstations with moderate memory requirements relative to the reference size.

In genomics workflows, BWA is a foundational aligner used to map reads before variant calling and other downstream analyses. It is widely cited in the literature and integrated with other tools such as SAMtools and the Genome Analysis Toolkit.