Accelerating Genome Sequencing 100-1000X with FPGAs

Conference · Tue Jan 01 00:00:00 EST 2008

OSTI ID:936292

Storaasli, Olaf O ^[1]

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1. ORNL

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Laboratory Directed Research and Development (LDRD) Program
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 936292
• Resource Relation: Conference: Many-core and Reconfigurable Supercomputing Conference (MRSC08), Belfast, Ireland, 20080401, 20080403
• Country of Publication: United States
• Language: English

Related Subjects

42 ENGINEERING
59 BASIC BIOLOGICAL SCIENCES
SUPERCOMPUTERS
SEMICONDUCTOR DEVICES
PERFORMANCE
DNA SEQUENCING
HUMAN CHROMOSOMES
F CODES
B CODES
Reconfigurable Computing
Field-Programmable Gate Arrays
FPGA
Science Applications
Genomics