Sambamba 0.6.6

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Sambamba offers the following features over SAMtools:

  • faster sort (no benchmarks yet, sorry)
  • automatic index creation when writing any coordinate-sorted file
  • view -L <bed file> utilizes BAM index to skip unrelated chunks
  • depth allows to measure base, sliding window, or region coverages
    • Chanjo builds upon this and gets you to exon/gene levels of abstraction
  • markdup, a fast implementation of Picard algorithm
  • slice quickly extracts a region into a new file, tweaking only first/last chunks

Accessing the software

To load the module:

$ module load Sambamba/0.6.6

An example command to include in your job script:

sambamba sort [OPTIONS] <input.bam>

where options can be found in the documentation and <input.bam> is an input BAM file.

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

None.

Other Information

The Support Level for this application is An.

Visit the website for more information regarding this application.


Last modified: 5 March 2018