Broad Institute of MIT and Harvard

Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks 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, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, Harvard-affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide.

Genome Analysis Toolkit (GATK)

Variant Discovery in High-Throughput Sequencing Data

Copyright Broad Institute, 2018. All rights reserved.

Developed in the Data Sciences Platform at the Broad Institute, GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

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Announcing GATK4 open source release

GATK4 logo credit: Susanna M. Hamilton, Broad Communications

“Releasing GATK4 as open source was the obvious next step for our team,” said Geraldine Van der Auwera, Associate Director of Outreach and Communications within the Data Science and Data Engineering group at the Broad Institute. “We believe it’s the most effective way to support the community, and we hope it continues to grow, innovate, and help researchers make insights that are essential for future human health breakthroughs.”

Read the blog “Foundation for the Future” by Anthony Philippakis, Chief Data Officer, Broad Institute of MIT and Harvard

Intel and Broad Deliver Genomics Stack

Photo Credit: Len Rubenstein and Broad Institute

Intel and Broad Institute introduce a new integrated hardware and software solution to run the Broad’s popular Genome Analysis Toolkit faster, at unprecedented scale, with easier open source deployment.

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Intel® Select Solutions for Genomics Analytics

Learn how Intel and Broad Institute are collaborating to advance computational genomics and analytics through hardware and software solutions.

Accelerate Genomics Research with the Broad-Intel Genomics Stack* (BIGstack*)

The highly-optimized BIGstack* with Intel® Xeon® Scalable processors and Intel® SSDs delivers an impressive throughput of up to 5 whole genomes per day per node, while using Intel® FPGA technology to accelerate analysis by up to 2.2x over prior-generation Intel® Xeon® processors and up to 1.8x over hard drives.

Learn how the Broad-Intel Genomics Stack* (BIGstack*), helps accelerate genomics research and whole genome sequencing.

Storing Genome Data as Sparse Columnar Arrays

Integrated into Broad Institute’s GATK, GenomicsDB is a storage technology for genomic variants and likelihoods. GenomicsDB uses columnar sparse arrays partitioned in a shared-nothing fashion across thousands of machines, enabling GATK’s joint genotyping workflow to scale to 100,000 samples and beyond. This allows bioinformaticians to achieve analysis results with high statistical confidence.

Additionally, using libraries optimized for Intel® architecture to compress data on disk, GenomicsDB cumulatively achieves orders of magnitude improvement in performance compared to existing tools.

Access GenomicsDB documentation at https://github.com/Intel-HLS/GenomicsDB/wiki

Accelerating Genomics Research with OpenCL™ and FPGAs

See how Intel and the Broad Institute are helping to accelerate genomics research with OpenCL™ and FPGAs running the GATK’s HaplotypeCaller algorithm.

This paper describes the acceleration of the GATK’s HaplotypeCaller using Intel’s FPGA devices, programmed using the Intel® FPGA SDK for OpenCL™ software technology. Upon integration with the GATK Best Practices pipeline, the overall pipeline speed-up was 1.2x compared to the Intel AVX technology implementation.

Learn More

Broad Institute, visit https://www.broadinstitute.org/
Genome Analysis Toolkit (GATK), visit https://software.broadinstitute.org/gatk/
GATK, get the source at https://software.broadinstitute.org/gatk/download/
Intel Broad Center for Genomic Engineering, visit www.intel.com/broadinstitute

Acknowledgements

Broad Institute: Geraldine Van der Auwera, Anthony Philippakis, Eric Banks, Stacey Gabriel, Eric Lander
Intel: Mark Bagley, Paolo Narvaez, Mishali Naik, Patrick Foley, Abirami Prabhakaran, Karthiq Gururaj, Stavros Papadopoulos, Kushal Datta, George Powley, Beri Shifaw, Ganapati Srinivasa, Ketan Paranjape, Eric Dishman, Jason Waxman, Diane Bryant
Marketing & Video Production: Josh Lemieux, Bryce Olson