CASAVA v1.8.2

The CASAVA 1.8.2 package processes sequencing reads provided by RTA or OLB. CASAVA v1.8.2 supports Nextera dual indexing. CASAVA can generate the following data:

  • Sample-specific reads from multiplexed flow cells
  • Aligned reads
  • SNP call
  • Indel calls
  • Expression levels for exons, genes and splice junctions in the RNA Sequencing analysis

In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples.CASAVA analyzes sequencing reads in three stages:

  • FASTQ file generation and demultiplexing
  • Alignment to a reference genome
  • Variant detection and counting

Accessing the software

To load the module:

$ module load apps/casava/v1.8.2

An example command to include in your job script:

CASAVA -a ExportExample

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 CASAVA website for more information regarding this application.


Last modified: 13 October 2017