BWA is a fast, light-weight tool that aligns relatively short sequences to a sequence database.  Itcomprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.


  • Website:
  • Li H and R Durbin, Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60 (2009). [PMID: 19451168]
  • H Li H and R Durbin, Fast and accurate long-read alignment with Burrows-Wheeler Transform.Bioinformatics, Epub. (2010). [PMID: 20080505]

Usage on Bridges-2

To see what versions of BWA are available and if there is more than one, which is the default, along with some help, type

module spider bwa

To use BWA, include a command like this in your batch script or interactive session to load the BWA module: (note ‘module load’ is case-sensitive):

module load BWA