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: http://bio-bwa.sourceforge.net/
- 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
Usage on Bridges
module help bwa
to see how to get usage information.
Include this command in your job script or interactive session:
module load bwa