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Impulse, Pico Computing Claim 16-fold Speed-Up of Broad's GATK Using FPGAs

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Impulse Accelerated Technologies and Pico Computing said recently that they have developed a proof-of-concept platform that achieves a 16-fold speed-up for the Broad Institute's Genome Analysis ToolKit using field-programmable gate array technology.

Brian Durwood, Impulse's CEO, said in a statement that his company is actively looking for research partners to further develop and commercialize this initial offering.

The companies said that they ran one of the workflows in the GATK on an M-501 FPGA-based acceleration module. The M-501, developed by Pico computing, is a small hardware module comprising an x8 Gen2 PCIe connected board and a Xilinx Virtex 6 FPGA.

Using this infrastructure, the developers parallelized the GATK framework to run as 12 individual streaming processes. They also made improvements to the parallel computing throughput using the Impulse C toolset developed by Impulse Accelerated Technologies.

The partners claimed that their FPGA-based implementation took 10.5 seconds to process some sample data compared to the software-only implementation of the GATK, which took 170 seconds.

Furthermore, this implementation uses less than half of the resources available on the FPGA and operates at 150 MHz, the partners said.

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