At Illumina, we are a dedicated to empowering your research through the continuous development of the most advanced genetic analysis tools. This rapid innovation occasionally results in product discontinuation, as we develop newer, more cutting-edge solutions. We are discontinuing distribution of CASAVA software, and will continue its support until December 31, 2015. We remain committed to providing you with the highest-quality support and service during this transition.

As a replacement for CASAVA, we have added functionality to the BaseSpace Isaac Enrichment and Isaac Whole Genome Sequencing apps available on BaseSpace and BaseSpace Onsite. In addition, the bcl2fastq Conversion Software is available to demultiplex and convert BCL files to FASTQ files on your local computer hardware. Illumina is committed to providing easy-to-operate, seamless solutions for the analysis of genomic data. BaseSpace and BaseSpace Onsite offer fully supported software solutions and are continuously optimized through ongoing development efforts.

CASAVA v1.8.2 Overview

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 calls
  • 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