Next-generation massively parallel short-read mapping on FPGAs

Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors

Volumn , Issue , 2011, Pages 195-201

  Knodel, Oliver ^a   Preusser, Thomas B ^a   Spallek, Rainer G ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

FPGA; Sequence Alignment; Short Read Mapping

Indexed keywords

ANALYSIS TOOLS; BOW TIE; EXACT RESULTS; GENOME DATABASE; PERFORMANCE COMPARISON; SEQUENCE ALIGNMENTS; SHEER SIZE; SHORT-READ MAPPING; STRING SEARCH; XILINX FPGA;

ALIGNMENT; DATABASE SYSTEMS; DNA; DNA SEQUENCES; GENE ENCODING; MOLECULAR BIOLOGY;

MAPPING;

EID: 80055076816     PISSN: 10636862     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ASAP.2011.6043268     Document Type: Conference Paper

References (21)

1. T. Smith and M. Waterman, "Identification of common molecular subsequences," Journal of molecular biology, vol. 147, no. 1, pp. 195-197, 1981.
2. S. Atschul, W. Gish, W. Miller, E. Myers, and D. Lipman, "Basic local alignment search tool," J. Mol. Biol, vol. 215, pp. 403-410, 1990.
3. J. Reis-Filho, "Next-generation sequencing," Breast Cancer Research, vol. 11, no. Suppl 3, p. S12, 2009.
4. M. Margulies, M. Egholm, W. Altman, S. Attiya, J. Bader, L. Bemben, J. Berka, M. Braverman, Y. Chen, Z. Chen et al., "Genome sequencing in microfabricated high-density picolitre reactors," Nature, vol. 437, no. 7057, pp. 376-380, 2005.
5. T. Ley, E. Mardis, L. Ding, B. Fulton, M. McLellan, K. Chen, D. Dooling, B. Dunford-Shore, S. McGrath, M. Hickenbotham et al., "Dna sequencing of a cytogenetically normal acute myeloid leukaemia genome," Nature, vol. 456, no. 7218, pp. 66-72, 2008.
6. E. Mardis, "The impact of next-generation sequencing technology on genetics," Trends in Genetics, vol. 24, no. 3, pp. 133-141, 2008.
7. B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, "Ultrafast and memory-efficient alignment of short dna sequences to the human genome," Genome Biology, vol. 10, no. 3, p. R25, 2009.
8. R. Li, C. Yu, Y. Li, T. Lam, S. Yiu, K. Kristiansen, and J. Wang, "Soap2: an improved ultrafast tool for short read alignment," Bioinformatics, vol. 25, no. 15, p. 1966, 2009.
9. H. Li, "Maq: Mapping and assembly with qualities," 2008, http://maq.sourceforge.net/.
10. D. Campagna, A. Albiero, A. Bilardi, E. Caniato, C. Forcato, S. Manavski, N. Vitulo, and G. Valle, "Pass: a program to align short sequences," Bioinformatics, vol. 25, no. 7, p. 967, 2009.
11. D. Weese, A. Emde, T. Rausch, A. Döring, and K. Reinert, "Razers - fast read mapping with sensitivity control," Genome research, vol. 19, no. 9, p. 1646, 2009.
12. P. Ferragina and G. Manzini, "Opportunistic data structures with applications," in focs. Published by the IEEE Computer Society, 2000, p. 390.
13. O. Owolabi and D. McGregor, "Fast approximate string matching," Software: Practice and Experience, vol. 18, no. 4, pp. 387-393, 1988.
14. C. Trapnell and S. Salzberg, "How to map billions of short reads on to genomes." Nature biotechnology, vol. 27, no. 5, p. 455, 2009.
15. I. Li, W. Shum, and K. Truong, "160-fold acceleration of the smith-waterman algorithm using a field programmable gate array(fpga)," BMC bioinformatics, vol. 8, no. 1, p. 185, 2007.
16. T. Oliver, B. Schmidt, and D. Maskell, "Hyper customized processors for bio-sequence database scanning on fpgas," in Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays. ACM, 2005, pp. 229-237.
17. S. Manavski and G. Valle, "Cuda compatible gpu cards as efficient hardware accelerators for smith-waterman sequence alignment," BMC bioinformatics, vol. 9, no. Suppl 2, p. S10, 2008.
18. M. Herbordt, J. Model, B. Sukhwani, Y. Gu, and T. VanCourt, "Single pass streaming blast on fpgas," Parallel computing, 2007.
19. E. Sotiriades, C. Kozanitis, and A. Dollas, "Fpga based architecture for dna sequence comparison and database search," in Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International. IEEE, 2006, pp. 8-pp.
20. Xilinx, "Virtex-6 libraries guide for HDL designs," http://www.xilinx.com/support/documentation/sw-manuals/xilinx12-3/virtex6-hdl. pdf, September 2010.
21. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin, "The sequence alignment/map format and samtools," Bioinformatics, vol. 25, no. 16, p. 2078, 2009.