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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