Pico Computing Accelerates BWA 48X

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Bioinformatics Application to be demonstrated at SC12.

M-505K325T + EX-500 + SC5 SuperCluster

Pico Computing will demonstrate its hardware accelerated Burrows-Wheeler Aligner (BWA) at the SC12 conference, to be held on November 10-16, 2012 in Salt Lake City, UT. For high throughput sequencing operations, BWA can take up to 8 hours to complete on commodity CPUs. However, with Pico’s hardware accelerated solution, this process has been reduced to less than 10 minutes resulting in a 4800% improvement.

In the past ten years, major improvements in DNA analysis have been made. With each improvement, the amount of data needing to be processed dramatically increases. One of the first stages when analyzing sequenced data is to map the short pieces, known as short reads, to a reference genome. This inexact matching process is commonly performed on commodity CPU clusters using a software package called BWA. As advancements in next generation sequencing technology continue to occur, the amount of computational requirements also continue to increase. As a result, the overhead costs associated with managing, updating and adding additional nodes to process the increasing amount of data have become an alarming concern.

Pico is proud to announce the BWA algorithm as its newest addition to their bioinformatics library. The solution from Pico comprises 12 M-505 FPGA modules in their SC5 SuperCluster. Pico has accelerated BWA by pushing some of the application logic into the M-505s and parallelizing the memory accesses to BWA’s index for increased memory bandwidth. Pico’s solution draws only 120 Watts. Comparatively, in order for commodity CPUs to achieve the performance levels of 12 M-505s, a total of 12 quad-core CPUs are required, drawing approximately 1.5 kilowatts.

“With a low-memory alignment algorithm like BWA, we can push the reference genome index into the DRAM local to each FPGA to efficiently parallelize memory lookups. Integrating all software command line options with our SC5 running BWA, researchers and biologists can seamlessly transition their workflows to our accelerated FPGA solution” said Paul Draghicescu, Software Engineer at Pico Computing.

To get more information or to see a live demonstration of Pico’s system in action, stop by booth 2107 during the SC12 conference. For product inquiries and pricing, please contact Pico Computing at Contact (at) picocomputing (dot) com.

About Pico Computing
Based in Seattle, Washington, Pico Computing specializes in highly integrated development and deployment platforms based on Field Programmable Gate Array (FPGA) technologies. Applications for Pico Computing technologies include cryptography, networking, signal processing, bioinformatics, and scientific computing. Pico Computing products are used in embedded systems as well as in military, national security, and high performance computing applications. For more information about Pico products and services, visit http://www.picocomputing.com.

About SC12
For 24 years, SC has been at the forefront in gathering the best and brightest minds in supercomputing together, with our unparalleled technical papers, tutorials, posters and speakers. SC12 will take a major step forward not only in supercomputing, but in super-conferencing, with everything designed to make the 2012 conference the most ‘you’ friendly conference in the world. We’re streamlining conference information and moving to a virtually real-time method of determining technical program thrusts. No more pre-determined technical themes picked far in advance. Through social media, data mining, and active polling, we’ll see which technical interests and issues emerge throughout the year, and focus on the ones that interest you the most.

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Cheyne Okawa
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