Exploring parallelism in short sequence mapping using burrows-wheeler transform

Proceedings of the 2010 IEEE International Symposium on Parallel and Distributed Processing, Workshops and Phd Forum, IPDPSW 2010

Volumn , Issue , 2010, Pages

  Bozdaǧ, Doruk ^a   Hatem, Ayat ^a,b   Catalyurek, Umit V ^a,b  

^a OHIO STATE UNIVERSITY   (United States)

^b The Ohio State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEST STRATEGY; BOW TIE; BURROWS WHEELER TRANSFORM; BURROWS-WHEELER TRANSFORMATION; DATA DISTRIBUTION; HIGH THROUGHPUT; MAPPING ALGORITHMS; MAPPING PROCESS; MAPPING TOOLS; PARALLEL EXECUTIONS; PARALLELIZATION STRATEGIES; RELATIVE EFFICIENCY; SHORT SEQUENCES; SPEED-UPS;

CONFORMAL MAPPING; DISTRIBUTED PARAMETER NETWORKS; WAVELET TRANSFORMS;

METADATA;

EID: 77954056397     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPSW.2010.5470897     Document Type: Conference Paper

References (17)

1. B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, "Ultrafast and memory-efficient alignment of short dna sequences to the human genome." Genome biology, vol. 10, no. 3, pp. R25+, 2009. [Online]. Available: http://dx.doi.org/10.1186/gb-2009-10-3-r25.
2. H. Li and R. Durbin, "Fast and accurate short read alignment with burrows-wheeler transform." Bioinformatics (Oxford, England), vol. 25, no. 14, pp. 1754-1760, July 2009. [Online]. Available: http://dx.doi.org/10.1093/ bioinformatics/btp324.
3. R. Li, C. Yu, Y. Li, T. W. Lam, S. M. Yiu, K. Kristiansen, and J. Wang, "SOAP2: an improved ultrafast tool for short read alignment." Bioinformatics (Oxford, England), vol. 25, no. 15, pp. 1966-1967, August 2009. [Online]. Available: http://dx.doi.org/10.1093/bioinformatics/btp336.
4. mapreads: SOLiD System Color Space Mapping Tool, Applied Biosystems, http://solidsoftwaretools.com/gf/project/mapreads/.
5. H. Li, J. Ruan, and R. Durbin, "Mapping short dna sequencing reads and calling variants using mapping quality scores." Genome research, vol. 18, no. 11, pp. 1851-1858, November 2008. [Online]. Available: http://dx.doi.org/10.1101/gr.078212.108.
6. A. D. Smith, Z. Xuan, and M. Q. Zhang, "Using quality scores and longer reads improves accuracy of solexa read mapping." BMC bioinformatics, vol. 9, no. 1, pp. 128+, February 2008. [Online]. Available: http://dx.doi.org/10.1186/1471-2105-9-128.
7. S. M. Rumble, P. Lacroute, A. V. Dalca, M. Fiume, A. Sidow, and M. Brudno, "Shrimp: Accurate mapping of short color-space reads," PLoS Comput Biol, vol. 5, no. 5, pp. e1 000 386+, May 2009. [Online]. Available: http://dx.doi.org/10.1371/journal.pcbi.1000386.
8. H. Lin, Z. Zhang, M. Q. Zhang, B. Ma, and M. Li, "ZOOM! zillions of oligos mapped." Bioinformatics (Oxford, England), vol. 24, no. 21, pp. 2431-2437, November 2008. [Online]. Available: http://dx.doi.org/10.1093/ bioinformatics/btn416.
9. C. Alkan, J. M. Kidd, T. Marques-Bonet, G. Aksay, F. Antonacci, F. Hormozdiari, J. O. Kitzman, C. Baker, M. Malig, O. Mutlu, S. C. Sahinalp, R. A. Gibbs, and E. E. Eichler, "Personalized copy number and segmental duplication maps using next-generation sequencing." Nature genetics, vol. 41, no. 10, pp. 1061-1067, October 2009. [Online]. Availablehttp://dx.doi.org/ 10.1038/ng.437.
10. B. D. Ondov, A. Varadarajan, K. D. Passalacqua, and N. H. Bergman, "Efficient mapping of applied biosystems solid sequence data to a reference genome for functional genomic applications," Bioinformatics, vol. 24, no. 23, pp. 2776-2777, December 2008. [Online]. Available: http://dx.doi.org/10. 1093/bioinformatics/btn512.
11. 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 (Oxford, England), vol. 25, no. 7, pp. 967-968, April 2009. [Online]. Available: http://dx.doi.org/10.1093/bioinformatics/btp087.
12. D. Bozdag, C. C. Barbacioru, and U. Catalyurek, "Parallel short sequence mapping for high throughput genome sequencing," in Proc. of the International Parallel and Distributed Processing Symposium, May 2009.
13. K. Davies, "Pacific Biosciences preparing the 15-minute genome by 2013," Bio IT World, Feb. 2008.
14. M. Burrows and D. J. Wheeler, "A block sorting lossless data compression algorithm," Technical report 124 Palo Alto, CA: Digital Equipment Corporation, 1994.
15. P. Ferragina and G. Manzini, "Opportunistic data structures with applications," in Proc. of the 41st Annual Symposium on Foundations of Computer Science, 2000.
16. T. Lam, W. Sung, S. Tam, C. Wong, and S. Yiu, "Compresses indexing and local alignment of dna," Bioinformatics, vol. 24, no. 6, pp. 791-797, 2008.
17. "Applied Biosystems SOLiD system," http://marketing. appliedbiosystems.com/mk/get/SOLID-KNOWLEDGE-LANDING.