CASAVA (DISABLED - will be removed on 12/22/17)

Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/22/17. If you need this software, please contact


Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software captures summary information for resequencing and counting studies and places the data in a compact structure for visualization within GenomeStudio Software or publicly available analysis tools. CASAVA can create genomic builds, call SNPs, detects indels, and count reads from data generated from one or more runs of the Genome Analyzer across a broad range of sequencing applications.

To run this software interactively in a Linux environment run the commands:
module load casava
CASAVA [options]
For a complete list of options, please visit the CASAVA homepage, or use the command
CASAVA --help
CASAVA also provides several Perl scripts for different functions which may be found in the directory
where VER is the module version of CASAVA you are using.
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