August 2008

Conference Paper

Accelerating Genome Sequencing 100-1000X with FPGAs

By:
Storaasli, Olaf O
Page Number:
1
Book Title:
Proceeding of Many-core and Reconfigurable Supercomputing Conference
Publication Date:
August 20, 2008
Publisher Location:
Queen's University, Belfast, Ireland
Conference Name:
Many-core and Reconfigurable Supercomputing Conference (MRSC08)
Conference Location:
Belfast, Ireland
Conference Sponsor:
Queen's University & Institute for Electrnics, Communications and Information Technology, Belfast

Abstract

The performance of FPGAs on Cray XD1 and SGI/RASC systems (with Virtex-II Pro 50 and Virtex-4 LX160 FPGAs) was evaluated for human genome sequencing using FASTA1 and BLAST2, respectively. Scalable speedups of 100X for a Virtex-4 FPGA (and exceeding 1000X for multiple FPGAs) over a 2.2 GHz Opteron were achieved. Similar FPGA speedups were achieved using BLAST on a SGI/RASC system at Oak Ridge National Laboratory.