CloudBurst: Highly sensitive read mapping with MapReduce

Bioinformatics

Volumn 25, Issue 11, 2009, Pages 1363-1369

  Schatz, Michael C ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BASE MISPAIRING; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE MAPPING; GENOME ANALYSIS; INTERMETHOD COMPARISON; MICROPROCESSOR; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DNA; GENOME; HUMANS; INTERNET; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 65649120715     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp236     Document Type: Article

References (20)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Baeza-yates,R.A. et al. (1992) Fast and practical approximate string matching. In Proceedings of the Combinatorial Pattern Matching, Third Annual Symposium. Tucson, AZ, pp. 185-192.
3. Bentley,D.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
4. Ghemawat,S. et al. (2003) The Google file system. In Proceedings of the Nineteenth ACM Symposium on Operating Systems Principles. ACM, Bolton Landing, NY, USA, pp. 29-43.
5. Gusfield,D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, England.
6. Dean,J. et al. (2008) MapReduce: Simplified data processing on large clusters. Commun. ACM, 51, 107-113.
7. Krishnaprasad,S. (2001) Uses and abuses of Amdahl's law. J. Comput. Small Coll., 17, 288-293.
8. Kurtz,S. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
9. Landau,G.M. et al. (1986) Introducing efficient parallelism into approximate string matching and a new serial algorithm. In Proceedings of the Eighteenth Annual ACM Symposium on Theory of Computing. ACM, Berkeley, CA, USA, pp. 220-230.
10. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10 R25.
11. Li,H. et al. (2008a) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18 1851-1858.
12. Li,R. et al. (2008b) SOAP: Short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
13. Lin,H. et al. (2008) ZOOM! zillions of oligos mapped. Bioinformatics, 24, 2431-2437.
14. Schatz,M.C. et al. (2007) High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics, 8, 474.
15. Shaffer,C. (2007) Next-generation sequencing outpaces expectations. Nat. Biotechnol., 25, 149.
16. Smith,T.F. et al. (1981) Identification of commonmolecular subsequences. J. Mol. Biol., 147, 195-197.
17. Smith,A.D. et al. (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9 128.
18. Venter,J.C. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
19. Wang,J. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
20. Wheeler,D.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.