The BAM format is an efficient method for storing and sharing data from modern, highly parallel sequencers. While primarily used for storing alignment information, BAMs can (and frequently do) store unaligned reads as well.

There are a growing number of general-purpose SAM/BAM manipulation programs, including SAMtools, Picard, and Bamtools. This tool is not intended to duplicate the complex suite of tasks those programs perform. Rather, it is simply intended to extract raw sequences (with qualities). We envision this tool being primarily useful to those wishing to duplicate or extend previous analyses.

Accessing the software

To load the module:

$ module load apps/bam2fastq/1.1.0

To view the command-line options for this application, run the following command:

$ bam2fastq --help

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the BAM2FASTQ website for more information regarding this application.

Last modified: 21 August 2017