Intel and the Broad Institute of MIT and Harvard have developed a new architecture, the Broad-Intel Genomics Stack (BIGstack), which delivers a five-times improvement to Broad’s genomics analytics pipeline using Intel’s CPUs, Omni-Path Fabric and SSDs.
The stack also includes optimisations for the forthcoming release of Intel’s integrated CPU + FPGA products.
Jason Waxman, corporate vice-president and GM: Data Centre Solutions Group at Intel, writes that China’s industry leader in genomics, BGI, will adopt most current GATK tools, including the Broad and Intel optimisations, in a groundbreaking step toward global alignment in the genomics community.
“Intel and Broad share the common vision of harnessing the power of genomic data and making it widely accessible for research around the world to yield important discoveries,” he states. “Genomics offers insights into the inner workings of DNA within organisms. Advances in genomics are fueling discovery-based research to better understand the complexities of biological systems.”
The new announcements herald new steps that can be taken toward understanding the molecular drivers of cancer and other diseases and accelerating the promise of precision medicine.
“That’s why Intel and Broad are making the BIGstack available to run the new GATK4 Best Practices pipeline up to five times faster than the previous versions, supporting data volumes at truly unprecedented scale and simplifying deployment with production-ready scripts.
“The architecture yields performance based on the combination of Intel CPUs, Omni-Path Fabric and SSDs. The BIGstack also includes optimisations for Intel FPGAs with early results showing a potential for more than 35-times improvement in the PairHMM algorithm.”
Version 1.0 of the Broad-Intel Genomics stack is now available to the 45 000 registered academic, nonprofit and commercial users of the GATK, the Broad’s popular genomics analysis toolkit.
Meanwhile, Broad has announced that it will open source Version 4 of GATK (GATK4), while BGI will provide access to GATK4, Broad’s workflow management system Cromwell and the WDL (workflow definition language) on the BGI Online platform with its cloud partner Alibaba Cloud in China.
The new turnkey solution will be available as a reference architecture and through original equipment manufacturers and system integrators.