De Novo assembly of high-throughput sequencing data with cloud computing and new operations on string graphs

Proceedings - 2012 IEEE 5th International Conference on Cloud Computing, CLOUD 2012

Volumn , Issue , 2012, Pages 155-161

  Chang, Yu Jung ^a   Chen, Chien Chih ^a,b   Ho, Jan Ming ^a   Chen, Chuen Liang ^b  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

bioinformatics cloud; de novo sequence assembly; map reduce

Indexed keywords

BUBBLE REMOVAL; COMPUTER SPEED; CONTIGS; DNA SEQUENCING; E. COLI; FASTER RATES; GRAPH CONSTRUCTION; GRAPH SIMPLIFICATION; HIGH-THROUGHPUT; LONG-PATH; MAP-REDUCE; MOORE'S LAW; PATH COMPRESSION; STRING GRAPHS; SUBGRAPHS; TOPOLOGY STRUCTURE;

ALGORITHMS; BIOINFORMATICS; CLOUD COMPUTING; DNA SEQUENCES; ESCHERICHIA COLI; GENES; TOPOLOGY;

DIRECTED GRAPHS;

EID: 84866746600     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CLOUD.2012.123     Document Type: Conference Paper

References (21)

1. J. R. Miller, S. Koren, and G. Sutton, "Assembly algorithms for next-generation sequencing data," Genoniics, vol. 95, no. 6, pp. 315-327, Jun. 2010.
2. P. A. Pevzner, H. Tang, and M. S. Waterman, "An Eulerian path approach to DNA fragment assembly," PNAS, vol. 98, no. 17, pp. 9748-9753, Aug. 2001.
3. E. W. Myers, "The fragment assembly string graph," Bioinformatics, vol. 21, no. suppl-2, pp. ii79-85, Sep. 2005.
4. D. R. Zerbino and E. Birney, "Velvet: algorithms for de novo short read assembly using de Bruijn graphs," Genome research, vol. 18, no. 5, p. 821, 2008.
5. M. J. Chaisson and P. A. Pevzner, "Short read fragment assembly of bacterial genomes," Genome Research, vol. 18, no. 2, p. 324, 2008.
6. J. Butler, I. MacCallum, M. Kleber, I. A. Shlyakhter, M. K. Belmonte, E. S. Lander, C. Nusbaum, and D. B. Jaffe, "ALLPATHS: De novo assembly of whole-genome shotgun microreads," Genome Research, vol. 18, no. 5, pp. 810-820, May 2008.
7. J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J. . Jones, and İ. Birol, "ABySS: A parallel assembler for short read sequence data," Genome Research, vol. 19, no. 6, p. 1117, 2009.
8. R. Li, H. Zhu, J. Ruan, W. Qian, X. Fang, Z. Shi, Y. Li, S. Li, G. Shan, K. Kristiansen, S. Li, H. Yang, J. Wang, and J. Wang, "De novo assembly of human genomes with massively parallel short read sequencing," Genome Res., Dec. 2009.
9. Y. Peng, H. Leung, S. Yiu, and F. Chin, "IDBA-A Practical Iterative de Bruijn Graph De Novo Assembler," in Research in Computational Molecular Biology, 2010, pp. 426-440.
10. M. Schatz, D. Sommer, D. Kelley, M. Pop, "Contrail: Assembly of Large Genomes using Cloud Computing,". http://contrail-bio.sf.net/.
11. D. Hernandez, P. François, L. Farinelli, M. Østerås, and J. Schrenzel, "De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer," Genome Research, vol. 18, no. 5, pp. 802-809, May 2008.
12. B. G. Jackson, P. S. Schnable, and S. Aluru, "Parallel short sequence assembly of transcriptomes," BMC Bioinformatics, vol. 10, no. Suppl 1, p. S14, Jan. 2009.
13. J. T. Simpson and R. Durbin, "Efficient construction of an assembly string graph using the FM-index," Bioinformatics, vol. 26, no. 12, pp. i367-373, Jun. 2010.
14. L. D. Stein, "The case for cloud computing in genome informatics," Genome Biology, vol. 11, no. 5, p.207, 2010.
15. Apache Hadoop project, http://hadoop.apache.org/.
16. J. Dean and S. Ghemawat, "MapReduce: simplified data processing on large clusters," Commun. ACM, vol. 51, no. 1, pp. 107-113, Jan. 2008.
17. T. White, "Hadoop: The Definitive Guide," O'Reilly Media, 2009.
18. J. Lin, C. Dyer, and G. Hirst, Data-Intensive Text Processing with MapReduce. Morgan and Claypool Publishers, 2010.
19. S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucleic Acids Research, vol. 25, no. 17, pp. 3389-3402, 1997.
20. P. Medvedev, K. Georgiou, G. Myers, and M. Brudno, "Computability of Models for Sequence Assembly," in Algorithms in Bioinformatics, vol. 4645, R. Giancarlo and S. Hannenhalli, Eds. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007, pp. 289-301.
21. Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, "A greedy algorithm for aligning DNA sequences," Journal of Computational Biology, vol. 7, no. 1-2, pp. 203-214, 2000.