St. Louis, MO — Appistry, a leading provider of big-data software solutions, announced today the availability of the first fully supported commercial release of the Broad Institute’s industry-standard NGS analysis software, the Genome Analysis Toolkit (GATK). The release marks the first official release of the software by Appistry, following the announcement last October that the Broad Institute had selected Appistry as the exclusive distributor of the GATK for use in a for-profit setting.

Appistry’s version 2013.1 of the toolkit, which was made available to customers on March 25, 2013, packages up into a single release all of the GATK updates, enhancements, and issue resolutions made by the Broad Institute since the preliminary commercial release from Appistry in December 2012. Appistry conducted extensive quality testing to enhance product stability and provide a high level of quality control. In addition, for those customers who want to try out the latest functionality from the Broad immediately, Appistry is making interim “beta” releases available between the quarterly, controlled updates. The interim releases provide functionality and product updates introduced by the Broad in its academic releases, but with the additional testing performed by Appistry for its controlled releases.

“Controlled releases from Appistry make the GATK easier to use in commercial settings, particularly regulated environments that require strict tracking of which software versions are in use,” said Trevor Heritage, vice president of sales and marketing for Appistry. “But we recognize that some commercial customers want the chance to try out the latest functionality from the Broad as it is released. Access to interim beta releases between the controlled releases will allow researchers in for-profit settings to access and work with the same GATK functionality that academics are using, on the same timeline.”

The new releases can be accessed through Appistry’s GATK Support Portal, which provides extensive documentation and support services to customers beyond that available from the Broad including a “Best Practices” guide to using the GATK for NGS variant calling. Appistry’s GATK Best Practices Guide organizes tips published by the Broad in multiple areas on its support forum and includes previously unpublished information on using the GATK discussed in Broad training sessions.

Appistry also announced that it is making the source code to the GATK available to customers to enable them to develop tools on top of the engine and integrate the GATK into their NGS systems, programs, and workflows. Access to the source code is provided as part of every Enterprise GATK license from Appistry, and users holding Lab, Workgroup, or Single-User licenses may purchase access to the source code for an additional fee.

Version 2013.1 of the GATK from Appistry includes Broad updates 2.2-16 to 2.4-9. These updates primarily build on the advanced functionality introduced to the GATK in August 2012, making Appistry version 2013.1 the fastest, best performing version of the GATK released to date. Enhancements and new functionality are as follows:

Base Quality Score Recalibration, which provides a calibrated error model from which to make mutation calls, is better at modeling small NGSsample sizes.

Both variant callers in the GATK (the Unified Genotyper and the Haplotype Caller) are faster. The Haplotype Caller, which performs local de novo assembly at suspected variant sites, now performs its careful assembly much faster than previous versions and provides more accurate SNP and indel calling than any other caller.

Reduce Reads compression, which can make a typical whole exome BAM file 100 times smaller for faster file sharing and analysis, now integrates consistently with the Haplotype Caller.

New and expanded tools for filtering data types, tabulating concordance results, refreshing genotype information in VCF files, and combining non-overlapping VCF files.

More information about the GATK from Appistry can be found at appistry.com/gatk.

About Appistry

Appistry orchestrates solutions to big data problems. Since 2001, Appistry’s fabric technology has empowered organizations and researchers to transform vast data into actionable intelligence. Appistry leverages its fabric to power Ayrris™, a big-data environment that weaves together high performance computing and analytics to provide the throughput and scale required for diverse applications—from discovering new medical therapies to delivering overnight packages, gaining clarity from financial transactions, or deciphering military satellite images. In 2012, Appistry was selected by the Broad Institute as the exclusive distributor of the GATK for use in a for-profit context.