Title :
MEMOCODE 2012 hardware/software codesign contest: DNA sequence aligner
Author :
Edwards, Stephen A.
Author_Institution :
Dept. of Comput. Sci., Columbia Univ., New York, NY, USA
Abstract :
The MEMOCODE design contest for 2012 is exact substring matching: a simplified form of the DNA sequence alignment problem. The challenge is to efficiently locate millions of 100-base-pair short read sequences in a 3-million-base-pair reference genome. Contestants had a month to create a fast system that ran on a given set of test data. Entries were judged both on absolute time and the product of time and system cost. The two winning groups, which were invited to contribute papers describing their solutions, judiciously chose algorithms that exploited powerful hardware. The two winning entries employed a hash algorithm running on a Convey HC-1 FPGA/multicore hybrid with an aggressive memory system and a Burrows-Wheeler/hash hybrid running on a 12-core Intel system was second.
Keywords :
DNA; biology computing; field programmable gate arrays; genomics; graphics processing units; hardware-software codesign; integrated circuit design; multiprocessing systems; pattern matching; storage management; 100-base-pair short read sequences; 12-core Intel system; 3-million-base-pair reference genome; Burrows-Wheeler-hash hybrid; Convey HC-1 FPGA-multicore hybrid; DNA sequence aligner; DNA sequence alignment problem; GPGPUs; MEMOCODE 2012 hardware-software codesign contest; aggressive memory system; exact substring matching; hash algorithm; Bioinformatics; DNA; Educational institutions; Genomics; Humans; Indexes; Runtime; DNA sequence alignment; FPGAs; GPGPUs; Multicore; hardware/software codesign; string matching;
Conference_Titel :
Formal Methods and Models for Codesign (MEMOCODE), 2012 10th IEEE/ACM International Conference on
Conference_Location :
Arlington, VA
Print_ISBN :
978-1-4673-1314-8
DOI :
10.1109/MEMCOD.2012.6292303
