To better support new products available on BaseSpace, Illumina is discontinuing distribution of CASAVA software. BaseSpace features analysis options for a large array of NGS applications. If you want to demultiplex and convert BCL files to FASTQ files, you can also use the bcl2fastq software. Illumina remains committed to providing you with high‑quality support and service during this transition.

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