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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.


Apache License Version 2.0


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of bam2fastq and load default version of bam2fastq as

module avail bam2fastq/ # list available modules
module load bam2fastq   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail bam2fastq

and choose explicit version you want to use.