Welcome!

News Feed Item

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.

More Stories By Business Wire

Copyright © 2009 Business Wire. All rights reserved. Republication or redistribution of Business Wire content is expressly prohibited without the prior written consent of Business Wire. Business Wire shall not be liable for any errors or delays in the content, or for any actions taken in reliance thereon.

Latest Stories
So, you bought into the current machine learning craze and went on to collect millions/billions of records from this promising new data source. Now, what do you do with them? Too often, the abundance of data quickly turns into an abundance of problems. How do you extract that "magic essence" from your data without falling into the common pitfalls? In her session at @ThingsExpo, Natalia Ponomareva, Software Engineer at Google, will provide tips on how to be successful in large scale machine lear...
SYS-CON Events announced today that Peak 10, Inc., a national IT infrastructure and cloud services provider, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Peak 10 provides reliable, tailored data center and network services, cloud and managed services. Its solutions are designed to scale and adapt to customers’ changing business needs, enabling them to lower costs, improve performance and focus inter...
In his session at @ThingsExpo, Chris Klein, CEO and Co-founder of Rachio, will discuss next generation communities that are using IoT to create more sustainable, intelligent communities. One example is Sterling Ranch, a 10,000 home development that – with the help of Siemens – will integrate IoT technology into the community to provide residents with energy and water savings as well as intelligent security. Everything from stop lights to sprinkler systems to building infrastructures will run ef...
SYS-CON Events announced today that DatacenterDynamics has been named “Media Sponsor” of SYS-CON's 18th International Cloud Expo, which will take place on June 7–9, 2016, at the Javits Center in New York City, NY. DatacenterDynamics is a brand of DCD Group, a global B2B media and publishing company that develops products to help senior professionals in the world's most ICT dependent organizations make risk-based infrastructure and capacity decisions.
Between the mockups and specs produced by analysts, and resulting applications built by developers, there exists a gulf where projects fail, costs spiral, and applications disappoint. Methodologies like Agile attempt to address this with intensified communication, with partial success but many limitations. In his session at 18th Cloud Expo, Charles Kendrick, CTO & Chief Architect at Isomorphic Software, will present a revolutionary model enabled by new technologies. Learn how business and devel...
You think you know what’s in your data. But do you? Most organizations are now aware of the business intelligence represented by their data. Data science stands to take this to a level you never thought of – literally. The techniques of data science, when used with the capabilities of Big Data technologies, can make connections you had not yet imagined, helping you discover new insights and ask new questions of your data. In his session at @ThingsExpo, Sarbjit Sarkaria, data science team lead ...
The IoT has the potential to create a renaissance of manufacturing in the US and elsewhere. In his session at 18th Cloud Expo, Florent Solt, CTO and chief architect of Netvibes, will discuss how the expected exponential increase in the amount of data that will be processed, transported, stored, and accessed means there will be a huge demand for smart technologies to deliver it. Florent Solt is the CTO and chief architect of Netvibes. Prior to joining Netvibes in 2007, he co-founded Rift Technol...
If there is anything we have learned by now, is that every business paves their own unique path for releasing software- every pipeline, implementation and practices are a bit different, and DevOps comes in all shapes and sizes. Software delivery practices are often comprised of set of several complementing (or even competing) methodologies – such as leveraging Agile, DevOps and even a mix of ITIL, to create the combination that’s most suitable for your organization and that maximize your busines...
Struggling to keep up with increasing application demand? Learn how Platform as a Service (PaaS) can streamline application development processes and make resource management easy.
New Relic, Inc. has announced a set of new features across the New Relic Software Analytics Cloud that offer IT operations teams increased visibility, and the ability to diagnose and resolve performance problems quickly. The new features further IT operations teams’ ability to leverage data and analytics, as well as drive collaboration and a common, shared understanding between teams. Software teams are under pressure to resolve performance issues quickly and improve availability, as the comple...
The proper isolation of resources is essential for multi-tenant environments. The traditional approach to isolate resources is, however, rather heavyweight. In his session at 18th Cloud Expo, Igor Drobiazko, co-founder of elastic.io, will draw upon their own experience with operating a Docker container-based infrastructure on a large scale and present a lightweight solution for resource isolation using microservices. He will also discuss the implementation of microservices in data and applicat...
See storage differently! Storage performance problems have only gotten worse and harder to solve as applications have become largely virtualized and moved to a cloud-based infrastructure. Storage performance in a virtualized environment is not just about IOPS, it is about how well that potential performance is guaranteed to individual VMs for these apps as the number of VMs keep going up real time. In his session at 18th Cloud Expo, Dhiraj Sehgal, in product and marketing at Tintri, will discu...
Join IBM June 8 at 18th Cloud Expo at the Javits Center in New York City, NY, and learn how to innovate like a startup and scale for the enterprise. You need to deliver quality applications faster and cheaper, attract and retain customers with an engaging experience across devices, and seamlessly integrate your enterprise systems. And you can't take 12 months to do it.
Machine Learning helps make complex systems more efficient. By applying advanced Machine Learning techniques such as Cognitive Fingerprinting, wind project operators can utilize these tools to learn from collected data, detect regular patterns, and optimize their own operations. In his session at 18th Cloud Expo, Stuart Gillen, Director of Business Development at SparkCognition, will discuss how research has demonstrated the value of Machine Learning in delivering next generation analytics to im...
This is not a small hotel event. It is also not a big vendor party where politicians and entertainers are more important than real content. This is Cloud Expo, the world's longest-running conference and exhibition focused on Cloud Computing and all that it entails. If you want serious presentations and valuable insight about Cloud Computing for three straight days, then register now for Cloud Expo.