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Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

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Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

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dc.contributor.author Tárraga, Joaquín es_ES
dc.contributor.author Arnau, Vicente es_ES
dc.contributor.author Martínez, Héctor es_ES
dc.contributor.author Moreno, Raúl es_ES
dc.contributor.author Cazorla, Diego es_ES
dc.contributor.author Salavert Torres, José es_ES
dc.contributor.author Blanquer Espert, Ignacio es_ES
dc.contributor.author Dopazo, Joaquín es_ES
dc.contributor.author Medina Castelló, Ignacio es_ES
dc.date.accessioned 2015-04-01T11:01:07Z
dc.date.available 2015-04-01T11:01:07Z
dc.date.issued 2014-09
dc.identifier.issn 1367-4803
dc.identifier.uri http://hdl.handle.net/10251/48631
dc.description.abstract HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20 for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies. es_ES
dc.description.sponsorship This work is supported by BIO2011-27069 and PRI-PIBIN-2011-1289 (Spanish Ministry of Economy and Competitiveness), the HPC4G initiative (http://www.hpc4g.org) and the Bull-CIPF Chair for Computational Genomics. en_EN
dc.language Inglés es_ES
dc.publisher Oxford University Press (OUP): Policy B - Oxford Open Option B es_ES
dc.relation.ispartof Bioinformatics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Sequence analysis es_ES
dc.subject.classification CIENCIAS DE LA COMPUTACION E INTELIGENCIA ARTIFICIAL es_ES
dc.title Acceleration of short and long DNA read mapping without loss of accuracy using suffix array es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1093/bioinformatics/btu553
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//BIO2011-27069/ES/UNDERSTANDING THE MECHANISMS OF THE DISEASE AND PRIORITIZING CANDIDATE GENES UNDER A SYSTEMS PERSPECTIVE/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//PRI-PIBIN-2011-1289/ES/Estudio de las bases moleculares del glaucoma mediante secuenciación de nueva generacion/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto de Instrumentación para Imagen Molecular - Institut d'Instrumentació per a Imatge Molecular es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació es_ES
dc.description.bibliographicCitation Tárraga, J.; Arnau, V.; Martínez, H.; Moreno, R.; Cazorla, D.; Salavert Torres, J.; Blanquer Espert, I.... (2014). Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. Bioinformatics. 30(23):3396-3398. https://doi.org/10.1093/bioinformatics/btu553 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1093/bioinformatics/btu553 es_ES
dc.description.upvformatpinicio 3396 es_ES
dc.description.upvformatpfin 3398 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 30 es_ES
dc.description.issue 23 es_ES
dc.relation.senia 269292
dc.identifier.eissn 1460-2059
dc.identifier.pmid 25143289 en_EN
dc.identifier.pmcid PMC4816028 en_EN
dc.description.references Biesecker, L. G. (2010). Exome sequencing makes medical genomics a reality. Nature Genetics, 42(1), 13-14. doi:10.1038/ng0110-13 es_ES
dc.description.references Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., … Notredame, C. (2011). BlastR—fast and accurate database searches for non-coding RNAs. Nucleic Acids Research, 39(16), 6886-6895. doi:10.1093/nar/gkr335 es_ES
dc.description.references Chaisson, M. J., & Tesler, G. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics, 13(1). doi:10.1186/1471-2105-13-238 es_ES
dc.description.references Chen, Y., Hong, J., Cui, W., Zaneveld, J., Wang, W., Gibbs, R., … Chen, R. (2013). CGAP-Align: A High Performance DNA Short Read Alignment Tool. PLoS ONE, 8(4), e61033. doi:10.1371/journal.pone.0061033 es_ES
dc.description.references Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., … Gingeras, T. R. (2012). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21. doi:10.1093/bioinformatics/bts635 es_ES
dc.description.references Fonseca, N. A., Rung, J., Brazma, A., & Marioni, J. C. (2012). Tools for mapping high-throughput sequencing data. Bioinformatics, 28(24), 3169-3177. doi:10.1093/bioinformatics/bts605 es_ES
dc.description.references Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. doi:10.1038/nmeth.1923 es_ES
dc.description.references Liu, C.-M., Wong, T., Wu, E., Luo, R., Yiu, S.-M., Li, Y., … Lam, T.-W. (2012). SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 28(6), 878-879. doi:10.1093/bioinformatics/bts061 es_ES
dc.description.references Manber, U., & Myers, G. (1993). Suffix Arrays: A New Method for On-Line String Searches. SIAM Journal on Computing, 22(5), 935-948. doi:10.1137/0222058 es_ES
dc.description.references McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., … DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303. doi:10.1101/gr.107524.110 es_ES
dc.description.references Raczy, C., Petrovski, R., Saunders, C. T., Chorny, I., Kruglyak, S., Margulies, E. H., … Tanner, S. W. (2013). Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics, 29(16), 2041-2043. doi:10.1093/bioinformatics/btt314 es_ES
dc.description.references Rognes, T., & Seeberg, E. (2000). Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics, 16(8), 699-706. doi:10.1093/bioinformatics/16.8.699 es_ES
dc.description.references Smith, T. F., & Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147(1), 195-197. doi:10.1016/0022-2836(81)90087-5 es_ES
dc.description.references Watson, M. (2014). Illuminating the future of DNA sequencing. Genome Biology, 15(2), 108. doi:10.1186/gb4165 es_ES


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