SC is the International Conference for
High Performance Computing, Networking,
Storage and Analysis

SCHEDULE: NOV 12-18, 2011

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FPGA Acceleration of Short Read Human Genome Mapping

SESSION: Applications II

EVENT TYPE: Exhibitor Forum

TIME: 4:30PM - 5:00PM

Presenter(s):Corey Olson

ROOM:WSCC 613/614

Field-programmable gate array (FPGA) based systems offer the potential for drastic improvement in the performance of data intensive applications. As a sample application we implemented the BFAST algorithm, which is a commonly used program for mapping DNA sequencing data to a reference genome. We developed a prototype system that achieves a greater than 14x speedup compared to the reference BFAST software running on dual quad core Xeons. We project that the final system will have a 692x improvement in system runtime and 513x improvement in power saving. We discuss how the algorithm was adapted to run on reconfigurable hardware and techniques used to achieve this acceleration.

Chair/Presenter Details:

Corey Olson - Pico Computing Inc.

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