Pittsburgh Supercomputing Center 

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BWA

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.

 

Documentation

  • 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

  • Bridges

  • BioU

Type 

module help bwa

to see how to get usage information.

Include this command in your job script

module load bwa

The BWA programs are availiable through the Galaxy instance on biou.

To make the BWA programs availiable through the command line, csh users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

To make the BWA programs availiable through the command line, bash users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

 

See more help for BWA