- -

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

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

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

Mostrar el registro completo del ítem

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

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/48631

Ficheros en el ítem

Thumbnail
Nombre: Joaquín;VICENTE ...
Tamaño: 107.5Kb
Formato: PDF
Descripción: Versión editorial
Abrir/Preview

Metadatos del ítem

Título: Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
Autor: Tárraga, Joaquín Arnau, Vicente Martínez, Héctor Moreno, Raúl Cazorla, Diego Salavert Torres, José Blanquer Espert, Ignacio Dopazo, Joaquín Medina Castelló, Ignacio
Entidad UPV: Universitat Politècnica de València. Instituto de Instrumentación para Imagen Molecular - Institut d'Instrumentació per a Imatge Molecular
Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació
Fecha difusión:
Resumen:
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 ...[+]
Palabras clave: Sequence analysis
Derechos de uso: Reconocimiento (by)
Fuente:
Bioinformatics. (issn: 1367-4803 ) (eissn: 1460-2059 )
DOI: 10.1093/bioinformatics/btu553
Editorial:
Oxford University Press (OUP): Policy B - Oxford Open Option B
Versión del editor: http://dx.doi.org/10.1093/bioinformatics/btu553
Código del Proyecto:
info:eu-repo/grantAgreement/MICINN//BIO2011-27069/ES/UNDERSTANDING THE MECHANISMS OF THE DISEASE AND PRIORITIZING CANDIDATE GENES UNDER A SYSTEMS PERSPECTIVE/
info:eu-repo/grantAgreement/MICINN//PRI-PIBIN-2011-1289/ES/Estudio de las bases moleculares del glaucoma mediante secuenciación de nueva generacion/
Agradecimientos:
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.
Tipo: Artículo

References

Biesecker, L. G. (2010). Exome sequencing makes medical genomics a reality. Nature Genetics, 42(1), 13-14. doi:10.1038/ng0110-13

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

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 [+]
Biesecker, L. G. (2010). Exome sequencing makes medical genomics a reality. Nature Genetics, 42(1), 13-14. doi:10.1038/ng0110-13

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

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

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

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

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

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. doi:10.1038/nmeth.1923

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

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

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

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

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

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

Watson, M. (2014). Illuminating the future of DNA sequencing. Genome Biology, 15(2), 108. doi:10.1186/gb4165

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem