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Old 04-15-2010, 07:54 AM   #1
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Location: pa

Join Date: Apr 2009
Posts: 32
Default Variant Confidence Scoring System added to NextGENe software

April 15, 2010, State College PA SoftGenetics announced the addition of a unique variant scoring system to its NextGENe software to assist researchers and clinicians utilizing Next Generation sequencing. The novel scoring system provides a confidence scoring based upon multiple factors such as depth of coverage, directionality balance, homopolymer presence as well as sequence direction with greater weighting being given to the 5’ end of the sequence.

The new NextGENe scoring system is applicable to sequences generated by all major 2nd generation platforms, Illumina GA, Roche Titanium GS as well as the AB SOLiD System.

“ When analyzing next-generation sequencing data” stated John McGuigan, Biologist at SoftGenetics, “there are many variables that affect the accuracy of mutation calls. The level of coverage, the fraction of reads with the mutation, and the fraction of reads aligned in the forward or reverse direction are always important. The possibility of misalignment as well as potential homopolymer errors in pyrosequencing data also need to be considered. This can be overwhelming for large alignments that may generate thousands of potential mutations. Considering multiple sources of error at once and generating an overall quality measurement is more useful than considering several aspects individually in an all-or-nothing mutation filter. It allows for increased specificity without reducing the sensitivity.”

NextGENe software, is a free standing, biologist-friendly Windows based analysis tool, requires no scripting, provides analysis modules for all typical applications and is compatible with data from all major 2nd generation sequencing platforms.

The company offers 30-day trials and no cost web-based training on its genetic analysis software packages. Interested parties may request the software on the company website: or via email:

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SoftGenetics, LLC specializes in the development of genetic analysis tools for both research and diagnostic applications. Hallmarks of SoftGenetics software tools are advanced technologies, providing exceptional accuracy, and sensitivity in an easy-to use Windows® user interface.

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