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.

Software Details

Version: 0.7.12 – Visit their website and view the support site

Licence: GPL v3

Application: Bioinformatics

Platform: Linux-64

Last Updated: May 12, 2015

Citation:

If you use the BWA-backtrack algorithm, please cite the following paper: Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]

* If you use the BWA-SW algorithm, please cite: Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595. [PMID: 20080505]

* If you use the fastmap component of BWA, please cite: Li H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28, 1838-1844. [PMID: 22569178]

* Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. [arXiv:1303.3997v2]

If you wish to use a different version of a program, or to request an upgrade to a newer version of existing software, please submit your request here.