Genome Analysis Toolkit Developed for Next-Generation Sequencing

Upon this engine, scientists have constructed a wide series of analysis tools to process data from any next-generation sequencing platform, and to identify changes in the sequences that may be associated with disease.

The Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (Boston, MA, USA) has chosen Appistry, Inc. (St. Louis, Mo, USA) to distribute the toolkit to users at for-profit companies one of the most widely used software for data processing and variant calling of next-generation sequencing data, and to provide those users with commercial-grade customer support.

First developed and introduced by the Broad Institute in 2009, the GATK user base has grown to include thousands of biomedical researchers, bioinformatics professionals, and clinicians from a wide-range of both nonprofit as well as for-profit organizations. The GATK has been used on initiatives ranging from the 1000 Genomes Project to the National Institutes of Health’s (NIH; Bethesda, MD, USA) Cancer Genome Atlas, and by many sequencing centers and leading researchers to conduct population studies and explore the genetic origins of disease.

“Genetic research is changing the face of modern healthcare, and tools like the GATK have been essential in making the reams of data coming off of sequencers actionable,” said Appistry chief executive officer Kevin Haar. “We are honored to have been chosen to help the Broad Institute bring GATK 2.0, with customer support, to for-profit users and ensure that it remains an important source of insight in deciphering the genetic code and better managing and treating human disease.”

The GATK framework supports a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its architecture, powerful processing engine, and high-performance, scalable computing capabilities enable it to work on projects of any size. GATK 2.0 brings considerable enhancement over earlier releases of the toolkit, including newer and more sophisticated tools for error modeling, data compression, and variant calling.

GATK 2.0 will continue to be freely available to non-profit users under an academic, nonprofit research license agreement. Appistry will make the toolkit available to users at for-profit companies under a separate license agreement with a subscription fee that will cover commercial-grade support for installation, configuration, and documentation as well as long-term support for each commercial release. GATK 1.0, now called GATK-lite, will remain free for all users.

“We have been thrilled that the GATK has proven useful to a diverse group of users. However, as an academic institution, we don’t have the resources to offer the level of support that many for-profit users of the GATK want and need,” said David Altshuler, deputy director of the Broad Institute. “By partnering with Appistry, we are able to continue to provide the toolkit for free to nonprofit users, and to continue to extend its capabilities, while also ensuring the kind of support that users at for-profit companies have been looking for.”

Appistry combines high performance computing and analytics to provide the throughput and scale required for diverse applications--from discovering new medical therapies to delivering overnight packages, decoding military satellite images, or gaining insights from financial transactions.

The Eli and Edythe L. Broad Institute of MIT and Harvard was founded in 2003 to empower this generation of creative scientists to transform medicine with new genome-based knowledge. The Broad Institute’s goal is to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, techniques, and data openly to the entire scientific community.

Related Links:
Broad Institute of the Massachusetts Institute of Technology and Harvard University
Appistry