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SYS-CON MEDIA Authors: Kevin Jackson, Peter Silva, Greg Wind, Glenn Rossman, Michael Jannery

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Appistry Releases Commercial Version of Broad Institute’s GATK 3

Appistry, Inc., a leading provider of high-performance computing and analytics solutions for next-generation medicine, today released the latest commercial version of the Broad Institute’s Genome Analysis Toolkit (GATK). GATK 3 provides new functionality and best practices to tackle modern challenges in next-generation sequencing (NGS) data analysis.

“The Broad Institute has described GATK 3 as a shift in the way they approach problems in NGS data analysis, as well as a shift in the scope of problems the toolkit can tackle,” said Trevor Heritage, vice president of corporate development and strategy at Appistry. For instance, a collection of enhancements to the GATK speeds the analysis of the large sample sets typically associated with observational clinical studies (cohorts). This is accomplished through two main updates:

  • An optimized algorithm achieved through a collaboration between the Broad Institute and Intel. The Broad says the optimization will enable scientists to conduct variant discovery three to five times faster than with prior versions of the GATK and to analyze a whole genome in one day rather than three.
  • A new pipeline that better supports large, multi-sample analysis. Rather than re-calling data for all samples in a study when new samples are added, scientists can now analyze the new samples as they are sequenced and combine these results with the stored results from the rest of the cohort.

Additionally, the GATK for the first time includes best-practice recommendations for calling variants from RNA sequencing, which has emerged as a critical source of information on cellular function and activity. The initial best practices focus on data processing and variant calling steps; recommendations for other key analysis steps will be introduced in future releases.

Appistry’s commercial release includes all functionality in GATK 3.1 released by the Broad on March 18, 2014. Appistry will demonstrate its release at booth #1844 at the annual meeting of the American Association for Cancer Research in San Diego, CA, from April 5-9, 2014. Appistry is also hosting a live webinar featuring the Broad Institute’s Geraldine Van der Auwera titled “Speed, Cohorts, and RNAseq: An Insider Look into GATK 3” on April 10, 2014. Register for the webinar at appistry.com/webinar.

About Appistry

A leading provider of high-performance computing and analytics for managing big data, Appistry empowers medical researchers, oncologists, and clinicians to capitalize on genomics medicine. Appistry is also the authorized provider Broad tools for next-generation sequencing analysis, making the tools easier to implement and use in for-profit settings. Learn more by following us on Facebook, Twitter, and LinkedIn.

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