To better support new products available on BaseSpace and BaseSpace Onsite, Illumina is discontinuing distribution of CASAVA software. BaseSpace and BaseSpace Onsite feature analysis options for a large array of NGS applications. Illumina remains committed to providing you with high‑quality support and service during this transition.

Latest Updates

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