Fast and accurate read mapping with approximate seeds and multiple backtracking

Nucleic Acids Research

Volumn 41, Issue 7, 2013, Pages

  Siragusa, Enrico ^a,b   Weese, David ^a   Reinert, Knut ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ANALYTICAL EQUIPMENT; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; FILTRATION; GENE LIBRARY; GENE MAPPING; GENE SEQUENCE; HUMAN; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENETIC VARIATION; GENOMICS; HUMANS; SOFTWARE;

EID: 84876548372     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt005     Document Type: Article

References (27)

1. Navarro, G., Baeza-Yates, R.A., Sutinen, E. and Tarhio, J. (2001) Indexing methods for approximate string matching. IEEE Data Eng. Bull., 24, 19-27.
2. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
3. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
4. Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
5. Navarro, G. (2001) A guided tour to approximate string matching. ACM Comput. Surv., 33, 31-88. (Pubitemid 33768480)
6. Weese, D., Holtgrewe, M. and Reinert, K. (2012) RazerS 3: faster, fully sensitive read mapping. Bioinformatics, 28, 2592-2599.
7. Ahmadi, A., Behm, A., Honnalli, N., Li, C., Weng, L. and Xie, X. (2012) Hobbes: optimized gram-based methods for efficient read alignment. Nucleic Acids Res., 40, e41.
8. Alkan, C., Kidd, J.M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J.O., Baker, C., Malig, M., Mutlu, O. et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-1067.
9. David, M., Dzamba, M., Lister, D., Ilie, L. and Brudno, M. (2011) SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics, 27, 1011-1012.
10. Manber, U. and Myers, G. (1990) Suffix arrays: a new method for on-line string searches. In: SODA, pp. 319-327.
11. Abouelhoda, M., Kurtz, S. and Ohlebusch, E. (2004) Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms, 2(1), 53-86.
12. Ferragina, P. and Manzini, G. (2001) An experimental study of an opportunistic index. In: Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, Washington, D.C., USA. Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, pp. 269-278.
13. Navarro, G. and Baeza-Yates, R. (2000) A hybrid indexing method for approximate string matching. J. Discrete Algorithms, 1, 205-239.
14. Myers, G. (1999) A fast bit-vector algorithm for approximate string matching based on dynamic programming. J. ACM, 46, 395-415.
15. Baeza-Yates, R.A. and Navarro, G. (1999) Faster approximate string matching. Algorithmica, 23, 127-158. (Pubitemid 129565528)
16. Morrison, D.R. (1968) PATRICIA-Practical algorithm to retrieve information coded in alphanumeric. J. ACM, 15, 514-534.
17. Weiner, P. (1973) Linear pattern matching algorithms. In: SWAT (FOCS) IEEE. IEEE Computer Society, Los Alamitos, CA, USA, pp. 1-11.
18. Ukkonen, E. (1995) On-line construction of suffix trees. Algorithmica, 14, 249-260.
19. Ukkonen, E. (1993) Approximate string-matching over suffix trees. In: Apostolico, A., Crochemore, M., Galil, Z. and Manber, U. (eds), Lecture Notes in Computer Science, Vol. 684. Springer Berlin Heidelberg, Ukkonen, Esko, pp. 228-242.
20. Baeza-Yates, R.A. and Gonnet, G.H. (1999) A fast algorithm on average for all-against-all sequence matching. In: SPIRE/CRIWG IEEE. IEEE Computer Society Press, pp. 16-23.
21. Dementiev, R., Kärkkäinen, J., Mehnert, J. and Sanders, P. (2008) Better external memory suffix array construction. J. Exp. Algorithmics, 12, 3.4:1-3.4:24.
22. Kasai, T., Lee, G., Arimura, H., Arikawa, S. and Park, K. (2001) Linear-time longest-common-prefix computation in suffix arrays and its applications. In: CPM. Springer-Verlag, London, UK, pp. 181-192. (Pubitemid 33298873)
23. Grossi, R., Gupta, A. and Vitter, J.S. (2003) High-order entropy-compressed text indexes. Proceedings of the 14th annual ACM-SIAM symposium on Discrete algorithms, Society for Industrial and Applied Mathematics SODA '03, Philadelphia, PA pp. 841-850.
24. Giegerich, R., Kurtz, S. and Stoye, J. (2003) Efficient implementation of lazy suffix trees. Softw. Pract. Exper., 33, 1035-1049.
25. Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
26. Holtgrewe, M., Emde, A.-K., Weese, D. and Reinert, K. (2011) A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics, 12, 210.
27. Holtgrewe, M. (2010) Mason- A read simulator for second generation sequencing data. Technical report TR-B-10-06, Institut fü r Mathematik und Informatik, Freie Universität Berlin.