Pico Computing to Demonstrate NextGen Sequencing Algorithms

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FPGA Clusters powers through NextGen Sequencing Algorithms.

Pico Computing will be demonstrating hardware accelerated Short Read Genome Mapping, Sequence Alignment Library, and Smith-Waterman at the Plant and Animal Genome Conference. The conference will held on January 16-19, 2010 at the Town and Country Convention Center in San Diego.

These sequencing algorithms will be running on Pico Computing’s High Performance FPGA systems, the M-501 and M-503 FPGA Modules. Both Modules are based on the Virtex-6 FPGA from Xilinx and feature up to 8GB of DDR3 and 27MB of QDRII SRAM local to the FPGA. These hardware accelerators allow for memory intensive applications, which traditionally could not be implemented to take advantage of the inherent parallel nature of FPGAs, to run at 400x to 1000x improvement over a standard CPU.

Short Read Genome Mapping: A joint project between Pico Computing and the University of Washington’s Computer Engineering Department, this hardware accelerated implementation resulted in a 400x speedup on Pico’s SC5 FPGA SuperCluster. In this implementation, BFAST is used to process each short read to find possible alignments (CALs), and then a fully gapped Smith-Waterman is used to score each CAL.

Sequence Alignment Library: Pico Computing will be exhibiting their sequence alignment library, which includes building blocks for customized sequence assembly algorithms. This library can be used to construct algorithms such as BFAST, GASSST, or even custom algorithms. The library makes full use of Pico's FPGA clusters to accelerate sequence assembly.

Smith-Waterman: Pico Computing will be demonstrating the Smith-Waterman algorithm on the M-503 Virtex-6 FPGA Module. Performance on a single M-503 is 50 Billion GCUPS. On Pico’s SC5 SuperCluster, up to 1.8 TCUPS can be achieved.

Pico Computing will demonstrate their FPGA hardware accelerators, Clusters and accelerated bioinformatics algorithms at the Plant and Animal Genome Conference exhibit area, booth #527.

About Pico Computing
Pico Computing, headquartered in Seattle, Washington, 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 the Plant and Animal Genome Conference
The Plant and Animal Genome Conference brings together the leading genetic scientists and researchers involved in plant and animal research and related areas. With over 50 countries represented, the Plant and Animal Genome Conference provides an established forum for the exchange of information internationally as well as domestically. http://www.intl-pag.org/

About the University of Washington
Located in Seattle, Washington was founded in 1891. The University of Washington is one the oldest state supported institutions on the West Coast and is one the preeminent research universities in the world.

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Mark Hur
Pico Computing Inc.
206-283-2178 ext. 107
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