BWA

Description

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Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Template:App Location Available versions:

• 0.5.9
• 0.5.10 (last 0.5 branch release)
• 0.6.0 (default, beware the changes that may be incompatible with 0.5 pipelines).

Running the application using modules

To use bwa with the environment modules system at HPC the following commands are available:

Get module information for bwa:

$module spider bwa

Load the default application module:

$module load bwa

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_BWA_DIR - directory where bwa is located.
• HPC_BWA_BIN - executable directory
• HPC_BWA_MAN - manpage directory
• HPC_BWA_DOC - documentation directory