Genome Analysis Toolkit 4 (GATK4) released as open source resource to accelerate research

Genome Analysis Toolkit 4 (GATK4) released as open source resource to accelerate research
Credit: Susanna M. Hamilton, Broad Communications

The Broad Institute of MIT in addition to Harvard will Discharge variation 4 of the industry-leading Genome Analysis Toolkit under an open source software license. The software package, designated GATK4, contains fresh tools in addition to rebuilt architecture. the item can be available currently as an alpha preview on the Broad Institute’s GATK website, having a beta Discharge expected in mid-June. Broad engineers announced the upgrade, as well as the decision to Discharge the tool as an open source product, at Bio-the item World today.


The fresh variation can be built on a fresh architecture, allowing significant streamlining of individual tools in addition to support for performance-enhancing technologies such as Apache SparkTM. This specific fresh framework brings improvements to parallelization, capitalizing on cloud deployment in addition to generating the process of analyzing vast amounts of genomic data easier, faster, in addition to more efficient.

“We wanted to remove traditional barriers of scale while offering the same high level of data quality our users expect,” said Eric Banks, Senior Director of Data Sciences in addition to Data Engineering at Broad in addition to a creator of the original GATK software package. “Thanks to the rapid adoption of cloud computing, researchers can finally do away with many of the infrastructure-related complications that will have hampered progress, especially at smaller institutions in addition to startups.”

Today, more than 45,000 academic in addition to commercial users worldwide rely on the GATK, running millions of analyses. The GATK can be the industry standard for identifying SNPs in addition to indels in germline DNA in addition to RNAseq data. In addition to improving the performance of these established tools, GATK4 extends This specific scope of analysis to include copy number in addition to structural variation, for both germline in addition to somatic research applications.

Fully open source software

GATK4 will be released as a fully open source product, thanks in part to a collaboration between Broad Institute in addition to Intel Corporation to advance high-performance analytics so researchers can study massive amounts of genomic data via diverse sources worldwide.

At the Intel-Broad Center for Genomic Data Engineering, software engineers in addition to researchers have spent the last several months building, optimizing, in addition to widely sharing fresh tools in addition to infrastructure to help scientists integrate in addition to process genomic data. GATK4 has benefited via This specific collaboration, which has helped engineers optimize best practices in hardware in addition to software for genome analytics to make the item possible to combine in addition to use research data sets that will reside on private, public, in addition to hybrid clouds.

“Releasing GATK4 as open source was the obvious next step for our team,” said Geraldine Van der Auwera, Associate Director of Outreach in addition to Communications within the Data Science in addition to Data Engineering group at the Broad Institute. “We believe the item’s the most effective way to support the community, in addition to we expect the item continues to grow, innovate, in addition to help researchers make insights that will are essential for future human health breakthroughs.” “the item can be critical for progress in biomedicine that will the software we use for analysing the genomes of millions of people can be robust in addition to well understood,” said Ewan Birney, Director of EMBL-EBI in addition to Chair of the Global Alliance for Genomics in addition to Health (GA4GH). “Releasing GATK software with an open source license directly supports open innovation, data re-use in addition to data re-analysis from the global biomedical community.”

“The GATK tools are crucial for both germline in addition to cancer analyses,” said Robert L. Grossman of the University of Chicago Department of Medicine in addition to an expert in biomedical informatics. “Releasing GATK4 as an open source software package will increase adoption, in addition to benefit the community.”

“Open sourcing the GATK can be a big deal for open genomics, in addition to for open science in general,” said Jeremy Freeman, manager of computational biology at the Chan Zuckerberg Initiative (CZI). “Not only does the item make This specific critical tool available to as broad as possible an audience for use, reuse, inspection, in addition to contribution—the item provides a powerful example to the community for how an existing project can embrace open source.”

“Open source code can be a foundation of efficient biomedical research,” said Brad Chapman, a research scientist at the Harvard T.H. Chan School of Public Health. “the item enables reproducibility, reuse in addition to remixing by removing barriers for sharing in addition to distributing analyses. The Broad Institute’s GATK team leads from the development of scalable, sensitive in addition to specific variant calling algorithms, in addition to open sourcing GATK4 will allow frameworks like Blue Collar Bioinformatics to make these methods broadly available to the scientific research community.”

“Cloudera has always been a supporter in addition to believer from the power of open source code,” said Tom White, data scientist at Cloudera in addition to a member of the Apache Hadoop PMC. “We’ve been excited to contribute to the GATK codebase, to make the item run smoothly on Apache Spark in addition to Cloudera. This specific next phase of the GATK, powered by Spark in addition to open source software, will expand access in addition to improve collaboration among genomic data scientists.”

“The open sourcing of GATK4 can be a great step for genomics, allowing for scalability in addition to performance gains to be openly available to the research, biotech in addition to pharmaceutical communities,” said Jason Waxman, corporate vice president in addition to general manager of Data Center Solutions at Intel. “GATK4, when run on Intel’s fresh reference architecture, can achieve a 5X speed-up compared to earlier versions of the software.”

“We at Google are excited to see This specific fresh Discharge,” said Ilia Tulchinsky, Google Cloud Healthcare Engineering Lead. “We’ve been collaborating with the Broad Institute for the past three years to enhance genomic processing on Google Cloud Platform. As a strong supporter for open source technology, we believe that will generating GATK available This specific way will facilitate its use by genomic scientists everywhere. As fellow collaborators with Intel, we particularly look forward to enabling researchers to run GATK4 on Google Cloud using the upcoming Intel Xeon processor Scalable family.”

“The GATK can be one of the most widely utilized software packages from the life sciences, in addition to our team has worked very productively with Broad to accelerate the item for use on Azure,” said Geralyn Miller, Director, AI & Research, Microsoft. “This specific fresh design will greatly facilitate This specific effort going forward, in addition to we are excited to continue in addition to expand our efforts around GATK on Azure.”

“With the open source launch of GATK4, there can be an opportunity to create a global community that will can collaborate together in addition to advance the state of art in bioinformatics,” said Hong Tang, chief architect at Alibaba Cloud, the cloud computing arm of Alibaba Group. “We look forward to closely working with Broad Institute in bringing the cloud-based GATK service to genomics customers in China, as well as in ongoing GATK research in addition to development.”

In addition to offering GATK4 as an open source toolkit, Broad Institute will continue to offer user support, training, in addition to outreach on its common user support forum. GATK4, like many of the Broad Institute’s genome analysis tools, will be available through the Broad Institute’s cloud based analysis platform, FireCloud.


Explore further:
Google joins effort to boost genomics research

Provided by:
Broad Institute of MIT in addition to Harvard

Genome Analysis Toolkit 4 (GATK4) released as open source resource to accelerate research

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