GATK on POWER

Today, Broad Institute announced the release of GATK on IBM POWER system. The HaplotypeCaller analysis can take a long time and this native implementation will leverage new POWER8 system to achieve performance optimization. The optimized code will run on Ubuntu 14 and RHEL7 platforms.

For more information and download the code, visit:

• https://www.broadinstitute.org/gatk/blog?id=4833
• http://gatkforums.broadinstitute.org/discussion/4833/speed-up-haplotypecaller-on-ibm-power8-systems

A big thanks to the IBM PowerGene development and ISV team for the work of optimization: Yinhe Cheng and Kathy Tzeng.

Also thanks to my friend Mauricio Carneiro, GATK development team manager, for allowing IBM to take on this challenge when we hatched the idea together during a genomics conference at Doha in June.

More Power to Genomics - scale, speed and SMARTS.

IBM Moves Big Irons for Next-Gen HPC

Earlier today US Department of Energy announced IBM has been awarded a $325 million contract to design and build two supercomputing systems, at Lawrence Livermore and Oak Ridge National Labs, both based on IBM's OpenPOWER technology.

As part of the announcement, Secretary of Energy Ernest Moniz and Sen. Lamar Alexander (R- Tenn.) hosted a press briefing at the US Capitol Building with John Kelly in attendance, along with multiple government leaders.

Notable quotes:

IBM can still move big iron. -Forbes

The systems to be installed at Lawrence Livermore and Oak Ridge will use future versions of IBM Power chip line to handle basic computation chores. -- Wall Street Journal

Both systems will be based on next-generation IBM POWER servers with NVIDIA's GPU accelerators and Mellanox's Interconnected technologies "to advance key research initiatives for national nuclear deterrence, technology advancement and scientific discovery," the DOE said. -- Business Standard

Optimized GATK Pipeline

We are wrapping up work and preparing to show case optimized GATK on Power8 next week at SC14. Besides SOAP pipeline, this will be another landmark for PowerGene::Genomics platform to support mission-critical genomics application.