SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Luo, Ruibang ^a   Wong, Thomas ^a   Zhu, Jianqiao ^a,e   Liu, Chi Man ^a   Zhu, Xiaoqian ^b   Wu, Edward ^a   Lee, Lap Kei ^a   Lin, Haoxiang ^c   Zhu, Wenjuan ^c   Cheung, David W ^a   Ting, Hing Fung ^a   Yiu, Siu Ming ^a   Peng, Shaoliang ^b   Yu, Chang ^c   Li, Yingrui ^c   Li, Ruiqiang ^d   Lam, Tak Wah ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

^c BGI SHENZHEN   (China)

^d PEKING UNIVERSITY   (China)

^e University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; COMPUTER; COMPUTER PROGRAM; CONTROLLED STUDY; GENE DELETION; GENE SEQUENCE; GENETIC DATABASE; GENETIC PROCEDURES; GRAPHICS PROCESSING UNIT; HUMAN; HUMAN GENOME; NEXT GENERATION SEQUENCING; SCORING SYSTEM; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SHORT READ ALIGNER;

EID: 84878532952     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065632     Document Type: Article

References (28)

1. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
2. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
3. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology 10: R25.
4. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
5. Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
6. Li Y, Zheng H, Luo R, Wu H, Zhu H, et al. (2011) Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol 29: 723-730.
7. Mullaney JM, Mills RE, Pittard WS, Devine SE, (2010) Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 19: R131-136.
8. Mu JC, Jiang H, Kiani A, Mohiyuddin M, Bani Asadi N, et al. (2012) Fast and accurate read alignment for resequencing. Bioinformatics 28: 2366-2373.
9. Liu Y, Schmidt B, (2012) Long read alignment based on maximal exact match seeds. Bioinformatics 28: i318-i324.
10. Marco-Sola S, Sammeth M, Guigo R, Ribeca P, (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods 9: 1185-1188.
11. Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson D, et al. (2011) Faster and More Accurate Sequence Alignment with SNAP. arXiv 1111.5572v1.
12. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
13. Nvidia (2012) Bioinformatics and Life Sciences.
14. Liu Y, Schmidt B, Maskell DL, (2012) CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics 28: 1830-1837.
15. Klus P, Lam S, Lyberg D, Cheung MS, Pullan G, et al. (2012) BarraCUDA- a fast short read sequence aligner using graphics processing units. BMC Res Notes 5: 27.
16. Liu CM, Wong T, Wu E, Luo R, Yiu SM, et al. (2012) SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 28: 878-879.
17. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
18. Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
19. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
20. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
21. Doring A, Weese D, Rausch T, Reinert K, (2008) SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics 9: 11.
22. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
23. Lam TW, Li R, Tam A, Wong S, Wu E, et al. High throughput short read alignment via bi-directional BWT; 2009. IEEE pp. 31-36.
24. Liu C, Lam T, Wong T, Wu E, Yiu S, et al. (2011) SOAP3: GPU-based compressed indexing and ultra-fast parallel alignment of short reads. The 3rd Workshop on Massive Data Algorithmics (MASSIVE 2011). Paris, France.
25. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
26. Liu Y, Maskell DL, Schmidt B, (2009) CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res Notes 2: 73.
27. Kim UJ, Shizuya H, de Jong PJ, Birren B, Simon MI, (1992) Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res 20: 1083-1085.
28. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272.