CASAVA

Latest Updates

• Improved Accuracy for ELAND and Variant Calling 06/05/2012

Guides

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