- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2014 (2014), Article ID 309650, 16 pages
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.
- J. Shendure and H. Ji, “Next-generation DNA sequencing,” Nature Biotechnology, vol. 26, no. 10, pp. 1135–1145, 2008.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- S. Q. Zhao, J. Wang, L. Zhang et al., “BOAT: basic oligonucleotide alignment tool,” BMC Genomics, vol. 10, 3, article S2, 2009.
- 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.
- 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.
- R. Li, Y. Li, K. Kristiansen, and J. Wang, “SOAP: short oligonucleotide alignment program,” Bioinformatics, vol. 24, no. 5, pp. 713–714, 2008.
- G. Rizk and D. Lavenier, “GASSST: global alignment short sequence search tool,” Bioinformatics, vol. 26, no. 20, pp. 2534–2540, 2010.
- 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.
- 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.
- 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.
- 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.
- 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.
- M. Farrar, “Striped Smith-Waterman speeds database searches six times over other SIMD implementations,” Bioinformatics, vol. 23, no. 2, pp. 156–161, 2007.
- H. Jiang and W. H. Wong, “SeqMap: mapping massive amount of oligonucleotides to the genome,” Bioinformatics, vol. 24, no. 20, pp. 2395–2396, 2008.
- D. Campagna, A. Albiero, A. Bilardi et al., “PASS: a program to align short sequences,” Bioinformatics, vol. 25, no. 7, pp. 967–968, 2009.
- 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.
- D. Weese, M. Holtgrewe, and K. Reinert, “RazerS 3: faster, fully sensitive read mapping,” Bioinformatics, vol. 28, no. 20, pp. 2592–2599, 2012.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- S. Descorps-Declère, D. Ziébelin, F. Rechenmann, and A. Viari, “Genepi: a blackboard framework for genome annotation,” BMC Bioinformatics, vol. 7, article 450, 2006.
- 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.
- 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.
- 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.
- H. Li and R. Durbin, “Fast and accurate long-read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 26, no. 5, pp. 589–595, 2010.
- H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009.
- 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.
- 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.
- S. Marguerat and J. Bähler, “RNA-seq: from technology to biology,” Cellular and Molecular Life Sciences, vol. 67, no. 4, pp. 569–579, 2010.
- 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.
- M. C. Schatz, “CloudBurst: highly sensitive read mapping with MapReduce,” Bioinformatics, vol. 25, no. 11, pp. 1363–1369, 2009.