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biobambam is a package of bioinformatics tools for processing BAM format files.  It has been installed on Breezy as a prerequisite for SMALT, but, the tools can be used independently. An initial test of bamtofastq found it an order of magnitude faster than the Picard Tools SamToFastq.

See the Software Versions page for details on the versions installed.

Restrictions / License Information

The software is distributed with the GNU General License Version 3.

Running biobambam on Breezy

Set up to use the biobambam package with (bash shell example):

export MANPATH=/global/software/biobambam/biobambam_0_0_92/man:$MANPATH
export PATH=/global/software/biobambam/biobambam_0_0_92/bin:$PATH

Help for individual tools is available through the man page or by running the command with the -h argument. For example:

man bamtofastq


bamtofastq -h

For More Information

Page created: 2014-02-20.

System Breezy
Version 0.0.92