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BioMed Research International
Volume 2014 (2014), Article ID 309650, 16 pages
http://dx.doi.org/10.1155/2014/309650
Research Article

Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis

1Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China
2Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
3School of Computer Science and Technology, Soochow University, Suzhou 215006, China

Received 17 December 2013; Accepted 4 February 2014; Published 23 March 2014

Academic Editor: Junfeng Xia

Copyright © 2014 Jing Shang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. Shendure and H. Ji, “Next-generation DNA sequencing,” Nature Biotechnology, vol. 26, no. 10, pp. 1135–1145, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. J. M. Otero, W. Vongsangnak, M. A. Asadollahi et al., “Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications,” BMC Genomics, vol. 11, no. 1, article 723, 2010. View at Publisher · View at Google Scholar · View at Scopus
  3. A. V. Dalca and M. Brudno, “Genome variation discovery with high-throughput sequencing data,” Briefings in Bioinformatics, vol. 11, no. 1, pp. 3–14, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. J. C. Marioni, C. E. Mason, S. M. Mane, M. Stephens, and Y. Gilad, “RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays,” Genome Research, vol. 18, no. 9, pp. 1509–1517, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. Y. Li, Z. Zhang, F. Liu, W. Vongsangnak, Q. Jing, and B. Shen, “Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis,” Nucleic Acids Research, vol. 40, no. 10, pp. 4298–4305, 2012. View at Publisher · View at Google Scholar
  6. D. S. Johnson, A. Mortazavi, R. M. Myers, and B. Wold, “Genome-wide mapping of in vivo protein-DNA interactions,” Science, vol. 316, no. 5830, pp. 1497–1502, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. T. A. Down, V. K. Rakyan, D. J. Turner et al., “A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis,” Nature Biotechnology, vol. 26, no. 7, pp. 779–785, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. S. J. Cokus, S. Feng, X. Zhang et al., “Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning,” Nature, vol. 452, no. 7184, pp. 215–219, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. S. Marguerat, B. T. Wilhelm, and J. Bähler, “Next-generation sequencing: applications beyond genomes,” Biochemical Society Transactions, vol. 36, part 5, pp. 1091–1096, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. 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, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Q. Zhao, J. Wang, L. Zhang et al., “BOAT: basic oligonucleotide alignment tool,” BMC Genomics, vol. 10, 3, article S2, 2009. View at Scopus
  12. Y. Chen, T. Souaiaia, and T. Chen, “PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds,” Bioinformatics, vol. 25, no. 19, pp. 2514–2521, 2009. View at Publisher · View at Google Scholar · View at Scopus
  13. R. Li, C. Yu, Y. Li et al., “SOAP2: an improved ultrafast tool for short read alignment,” Bioinformatics, vol. 25, no. 15, pp. 1966–1967, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. R. Li, Y. Li, K. Kristiansen, and J. Wang, “SOAP: short oligonucleotide alignment program,” Bioinformatics, vol. 24, no. 5, pp. 713–714, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. G. Rizk and D. Lavenier, “GASSST: global alignment short sequence search tool,” Bioinformatics, vol. 26, no. 20, pp. 2534–2540, 2010. View at Publisher · View at Google Scholar · View at Scopus
  16. 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, article 128, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. W. Zhang, J. Chen, Y. Yang, Y. Tang, J. Shang, and B. Shen, “A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies,” PLoS ONE, vol. 6, no. 3, Article ID e17915, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. 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, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Hoffmann, C. Otto, S. Kurtz et al., “Fast mapping of short sequences with mismatches, insertions and deletions using index structures,” PLoS Computational Biology, vol. 5, no. 9, Article ID e1000502, 2009. View at Publisher · View at Google Scholar · View at Scopus
  20. P. Flicek and E. Birney, “Sense from sequence reads: methods for alignment and assembly,” Nature Methods, vol. 6, no. 11, supplement, pp. S6–S12, 2009. View at Scopus
  21. M. Farrar, “Striped Smith-Waterman speeds database searches six times over other SIMD implementations,” Bioinformatics, vol. 23, no. 2, pp. 156–161, 2007. View at Publisher · View at Google Scholar · View at Scopus
  22. H. Jiang and W. H. Wong, “SeqMap: mapping massive amount of oligonucleotides to the genome,” Bioinformatics, vol. 24, no. 20, pp. 2395–2396, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. D. Campagna, A. Albiero, A. Bilardi et al., “PASS: a program to align short sequences,” Bioinformatics, vol. 25, no. 7, pp. 967–968, 2009. View at Publisher · View at Google Scholar · View at Scopus
  24. D. Weese, A. Emde, T. Rausch, A. Döring, and K. Reinert, “RazerS—fast read mapping with sensitivity control,” Genome Research, vol. 19, no. 9, pp. 1646–1654, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. D. Weese, M. Holtgrewe, and K. Reinert, “RazerS 3: faster, fully sensitive read mapping,” Bioinformatics, vol. 28, no. 20, pp. 2592–2599, 2012. View at Publisher · View at Google Scholar
  26. C. Alkan, J. M. Kidd, T. Marques-Bonet et al., “Personalized copy number and segmental duplication maps using next-generation sequencing,” Nature Genetics, vol. 41, no. 10, pp. 1061–1067, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. F. Hach, F. Hormozdiari, C. Alkan et al., “MrsFAST: a cache-oblivious algorithm for short-read mapping,” Nature Methods, vol. 7, no. 8, pp. 576–577, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. K. Schneeberger, J. Hagmann, S. Ossowski et al., “Simultaneous alignment of short reads against multiple genomes,” Genome Biology, vol. 10, no. 9, article R98, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. C. Trapnell and S. L. Salzberg, “How to map billions of short reads onto genomes,” Nature Biotechnology, vol. 27, no. 5, pp. 455–457, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. S. M. Rumble, P. Lacroute, A. V. Dalca, M. Fiume, A. Sidow, and M. Brudno, “SHRiMP: accurate mapping of short color-space reads,” PLoS Computational Biology, vol. 5, no. 5, Article ID e1000386, 2009. View at Publisher · View at Google Scholar · View at Scopus
  31. M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno, “SHRiMP2: sensitive yet practical short read mapping,” Bioinformatics, vol. 27, no. 7, pp. 1011–1012, 2011. View at Publisher · View at Google Scholar · View at Scopus
  32. S. Schbath, V. Martin, M. Zytnicki, J. Fayolle, V. Loux, and J. F. Gibrat, “Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis,” Journal of Computational Biology, vol. 19, no. 6, pp. 796–813, 2012. View at Publisher · View at Google Scholar
  33. H. Lin, Z. Zhang, M. Q. Zhang, B. Ma, and M. Li, “ZOOM! zillions of oligos mapped,” Bioinformatics, vol. 24, no. 21, pp. 2431–2437, 2008. View at Publisher · View at Google Scholar · View at Scopus
  34. N. Homer, B. Merriman, and S. F. Nelson, “BFAST: an alignment tool for large scale genome resequencing,” PLoS ONE, vol. 4, no. 11, Article ID e7767, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. S. Descorps-Declère, D. Ziébelin, F. Rechenmann, and A. Viari, “Genepi: a blackboard framework for genome annotation,” BMC Bioinformatics, vol. 7, article 450, 2006. View at Publisher · View at Google Scholar · View at Scopus
  36. K. Daily, P. Rigor, S. Christley, X. Xie, and P. Baldi, “Data structures and compression algorithms for high-throughput sequencing technologies,” BMC Bioinformatics, vol. 11, article 514, 2010. View at Publisher · View at Google Scholar · View at Scopus
  37. 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, article R25, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. T. W. Lam, W. K. Sung, S. L. Tam, C. K. Wong, and S. M. Yiu, “Compressed indexing and local alignment of DNA,” Bioinformatics, vol. 24, no. 6, pp. 791–797, 2008. View at Publisher · View at Google Scholar · View at Scopus
  39. H. Li and R. Durbin, “Fast and accurate long-read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 26, no. 5, pp. 589–595, 2010. View at Publisher · View at Google Scholar · View at Scopus
  40. H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. N. L. Clement, Q. Snell, M. J. Clement et al., “The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing,” Bioinformatics, vol. 26, no. 1, pp. 38–45, 2009. View at Publisher · View at Google Scholar · View at Scopus
  42. Z. Ning, A. J. Cox, and J. C. Mullikin, “SSAHA: a fast search method for large DNA databases,” Genome Research, vol. 11, no. 10, pp. 1725–1729, 2001. View at Publisher · View at Google Scholar · View at Scopus
  43. S. Marguerat and J. Bähler, “RNA-seq: from technology to biology,” Cellular and Molecular Life Sciences, vol. 67, no. 4, pp. 569–579, 2010. View at Publisher · View at Google Scholar · View at Scopus
  44. C. M. Liu, T. Wong, E. Wu et al., “SOAP3: ultra-fast GPU-based parallel alignment tool for short reads,” Bioinformatics, vol. 28, no. 6, pp. 878–879, 2012. View at Publisher · View at Google Scholar · View at Scopus
  45. M. C. Schatz, “CloudBurst: highly sensitive read mapping with MapReduce,” Bioinformatics, vol. 25, no. 11, pp. 1363–1369, 2009. View at Publisher · View at Google Scholar · View at Scopus