Broad collaboration with Intel Bio Team

We're very excited to announce that we have started collaborating with a team from Intel (yep, that Intel) to optimize key parts of the GATK code to make it run faster. The first fruits of this collaboration --a set of hardware-based optimizations for the PairHMM algorithm in HaplotypeCaller-- are available as of today in version 3.1 of the GATK. Please see the release notes and version highlights in the Version History section of the Guide for details.

Of course this is only the beginning, and we're looking forward to delivering more performance improvements for various other GATK tools moving forward as part of this collaboration.

What's really cool is that this collaboration extends beyond our little GATK team; the Intel Bio Team is also going to be working with other groups at the Broad Institute to make their software run faster as well, all with the goal of accelerating scientific research and discovery.

For more details and background information, see the Bio-IT World story here:

Comment on this article in the forum

Search blog by tag

2013 ad agbt14 appistry baserecalibrator belgium best-practices blog bqsr broken-links brussels bug bug-fixed cancer catvariants challenge combinegvcfs combinevariants commercial community compbio competition conferences depthofcoverage diagnosetargets documentation downtime error fastaalternatereferencemaker forum gatk gatk-3-0 gatk-3-1 gatk-3-2 gatk-lite gatk2 gatk3 genotypegvcfs gsa gsa-announce gvcf haplotypecaller hardware holiday indelrealigner intel job job-offer jobs joint-analysis joint-discovery key license lite media meetings multisample multithreading mutect nt optimization pairhmm paper performance phone-home pipeline poster presentations press printreads queue randomlysplitvariants readbackedphasing reducereads reference-model release release-notes rnaseq scatter-gather selectvariants slides spam splitncigarreads support talks topstory trivia tutorials unifiedgenotyper userstories validatevariants variantannotator varianteval variantrecalibrator variantstobinaryped version-highlights video videos webinar workshop

GATK Dev Team


RT @edgenome: Today's attendees at our 'Linux for Genomics' workshop. Keep tuned for more info on forthcoming courses and events... http://…
25 Jul 14
RT @TheAllium: Broad Institute “Can’t be bothered anymore” with donations below $200 Million via @theallium
24 Jul 14
RT @appistry: Join us tomorrow for our #webinar discussing the #PickMyPipeline Challenge! #NGS
23 Jul 14
New Pipeline Challenge from @Appistry
23 Jul 14
@Elfsevier @jermdemo Isn't bro-ness itself a disease? Or do you mean diseases that are comorbid to bro-ness?
22 Jul 14