Intel has partnered with the Broad Institute to optimize the latest version of the Broad’s Genome Analysis Toolkit (GATK) 3.1 for Intel Advanced Vector Extensions (Intel AVX) in Intel Xeon-powered servers.
Thanks to the partnership the companies are able to achieve three to five times overall improvement in variant discovery to meet the challenges of research and accelerate discovery.
Together with new methods, GATK 3.1 can now analyze data sets consisting of tens of thousands of DNA samples – a hundred times improvement over what was previously achievable.
The improved speed for variant analysis in large association studies will help enable new medical discoveries never before thought possible for conditions such as cancer, neurodegenerative disorders and cardiovascular disease, the company claims.
As part of a recently formed collaboration between Intel and the Broad Institute’s Genomics Platform, Intel helped improve the performance of Broad’s GATK software by using Intel AVX.
The GATK 3.1 is a new software package developed at the Broad Institute to analyze next-generation re-sequencing data. It features powerful processing engine and high-performance computing features to make it capable of taking on projects of any size.
Intel AVX is a 256-bit instruction set extension to Intel SSE found in Intel platforms and is designed for applications that are highly compute-intensive. It improves performance, better manages data in applications like image, audio/video processing, scientific simulations, financial analytics and 3D modeling and analysis.