Accelerating millions of short reads mapping on a heterogeneous architecture with FPGA accelerator

Proceedings of the 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines, FCCM 2012

Volumn , Issue , 2012, Pages 184-187

  Tang, Wen ^a,b   Wang, Wendi ^a,b   Duan, Bo ^a,b   Zhang, Chunming ^a   Tan, Guangming ^a   Zhang, Peiheng ^a   Sun, Ninghui ^a  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

accelerator; FPGA; hash; short reads mapping

Indexed keywords

BASIC OPERATION; CURRENT COMPUTING; HASH; HETEROGENEOUS ARCHITECTURES; MAPPING ALGORITHMS; PROCESSING ELEMENTS; PROPOSED ARCHITECTURES;

ACCELERATION; COMPUTERS; CONFORMAL MAPPING; DATA TRANSFER; PARTICLE ACCELERATORS;

FIELD PROGRAMMABLE GATE ARRAYS (FPGA);

EID: 84864961254     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FCCM.2012.39     Document Type: Conference Paper

References (13)

1. Illumina, "HiSeq 2000 Sequencing System", http://www.illumina. com/
2. Life Technologies, "5500 Series Genetic Analysis Systems", http://www.appliedbiosystems.com/
3. Li H, Homer N, "A survey of sequence alignment algorithms for next-generation sequencing," Brief Bioinform 2010, 11:473-83.
4. Kent, J.W., "BLAT-The BLAST-Like Alignment Tool," Genome Res. 12(4), 656-664, 2002.
5. Chen Y, Souaiaia T, Chen T. "PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds," Bioinformatics 2009;25:2514-21.
6. N. Tuck, T. Sherwood, B. Calder, and G. Varghese, "Deterministic memory-efficient string matching algorithms for intrusion detection," IEEE Infocom 2004, pp. 333-340.
7. NCBI, http://www.ncbi.nlm.nih.gov/
8. Novogenne, http://www.novogene.cn/
9. Fernandez, E.; Najjar, W.; Harris, E.; Lonardi, S.; , "Exploration of Short Reads Genome Mapping in Hardware," Field Programmable Logic and Applications (FPL), 2010 International Conference on , pp.360-363, Aug. 31 2010-Sept. 2 2010.
10. Brewer, T.M.; , "Instruction Set Innovations for the Convey HC-1 Computer," Micro, IEEE , vol.30, no.2, pp.70-79, March-April 2010.
11. Nathan Clement, Mark J. Clement, Quinn Snell, W. Evan Johnson, "Parallel Mapping Approaches for GNUMAP," in IPDPS'11: Tenth IEEE International Workshop on High Performance Computational Biology, May 2011.
12. Ashwin M. Aji, Liqing Zhang, and Wu-chun Feng, "GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors," In Proceedings of the 2010 13th IEEE International Conference on Computational Science and Engineering (CSE '10).
13. Fernandez, E.; Najjar, W.; Harris, E.; Lonardi, S.; , "String Matching in Hardware Using the FM-Index," in Field-Programmable Custom Computing Machines(FCCM), 2011 IEEE 19th Annual International Symposium on, pp. 218-225, May 1-3 2011.