THE NEWEST version of SoftGenetics’s NextGene software includes a module for copy number variation (CNV) and a user selectable reporting functions among its enhancements.
NextGene 2.3.1 includes the CNV analysis tool, which uses a proprietary method to normalise coverage between two samples. A list of heterozygous SNPs with approximately 50 percent allele is generated for each sample, and the median is used to normalise two samples on a global level.
A representative position is then selected for each region and used to calculate a log2 ratio and confidence score. When selecting a position for comparison, a heterozygous mutation in one sample is preferred so that any allele frequency changes can be used to examine potential loss of heterozygosity.
This new custom reporting option provides the capability to tailor reporting to meet specific needs.
NextGene is described as a comprehensive, free-standing Windows program for all next-generation sequencing (NGS) platforms. The user interface requires no scripting, provides graphical reporting, multiple analysis comparison, and causative prediction from multiple functional prediction databases including Cosmic, dbNSFP, PolyPhen, and others.
SoftGenetics offers 30-day free trials and no-cost web-based training on its software.