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Highly sensitive and ultrafast read mapping for RNA-seq analysis

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Highly sensitive and ultrafast read mapping for RNA-seq analysis

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dc.contributor.author Medina, I. es_ES
dc.contributor.author Tárraga, J. es_ES
dc.contributor.author Martínez, H, es_ES
dc.contributor.author Barrachina, S. es_ES
dc.contributor.author Castillo, M. I. es_ES
dc.contributor.author Paschall, J. es_ES
dc.contributor.author Salavert Torres, José es_ES
dc.contributor.author Blanquer Espert, Ignacio es_ES
dc.contributor.author Hernández García, Vicente es_ES
dc.contributor.author Quintana Ortí, Enrique Salvador es_ES
dc.contributor.author Dopazo, J. es_ES
dc.date.accessioned 2016-04-18T07:25:36Z
dc.date.available 2016-04-18T07:25:36Z
dc.date.issued 2016-01
dc.identifier.issn 1340-2838
dc.identifier.uri http://hdl.handle.net/10251/62698
dc.description.abstract As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available. es_ES
dc.description.sponsorship This work is supported by grants from the Spanish Ministry of Economy and Competitiveness (BIO2014-57291-R) and co-funded with European Regional Development Funds (ERDF), AECID (D/016099/08) and from the Conselleria d'Educacio of the Valencian Community (PROMETEOII/2014/025). This work has been carried out in the context of the HPC4G initiative (http://www.hpc4g.org) and the Bull-CIPF Chair for Computational Genomics. Funding to pay the Open Access publication charges for this article was provided by grant BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness (MINECO), co-funded with European Regional Development Funds (ERDF). en_EN
dc.language Inglés es_ES
dc.publisher Oxford University Press es_ES
dc.relation.ispartof DNA Research es_ES
dc.rights Reconocimiento - No comercial (by-nc) es_ES
dc.subject RNA-seq es_ES
dc.subject Mapping es_ES
dc.subject Burrows-Wheeler Transform es_ES
dc.subject High-performance computing es_ES
dc.subject.classification CIENCIAS DE LA COMPUTACION E INTELIGENCIA ARTIFICIAL es_ES
dc.title Highly sensitive and ultrafast read mapping for RNA-seq analysis es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1093/dnares/dsv039
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BIO2014-57291-R/ES/NUEVAS ESTRATEGIAS PARA EL DESCUBRIMIENTO DE DIANAS MOLECULARES Y DISEÑO DE NUEVAS APROXIMACIONES TERAPEUTICAS CONTRA EL CANCER Y OTRAS ENFERMEDADES BASADAS EN BIOLOGIA DE SIS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MAEC//D%2F016099%2F08/ES/ACCION PARA EL FORTALECIMIENTO CIENTÍFICO TECNOLÓGICO EN ÁREAS RELACIONADAS CON LA GENÓMICA Y BIOINFORMÁTICA APLICADAS A LOS SISTEMAS AGROPECUARIOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GVA//PROMETEOII%2F2014%2F025/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Informática de Sistemas y Computadores - Departament d'Informàtica de Sistemes i Computadors 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.description.bibliographicCitation Medina, I.; Tárraga, J.; Martínez, H.; Barrachina, S.; Castillo, MI.; Paschall, J.; Salavert Torres, J.... (2016). Highly sensitive and ultrafast read mapping for RNA-seq analysis. DNA Research. 1(1):1-8. https://doi.org/10.1093/dnares/dsv039 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/ 10.1093/dnares/dsv039 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 8 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 1 es_ES
dc.description.issue 1 es_ES
dc.relation.senia 298896 es_ES
dc.identifier.pmid 26740642 en_EN
dc.identifier.pmcid PMC4833417 en_EN
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder Ministerio de Asuntos Exteriores y Cooperación es_ES
dc.contributor.funder Generalitat Valenciana es_ES
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