Highly sensitive and ultrafast read mapping for RNA-seq analysis

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 a...

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Detalles Bibliográficos
Autores principales: Medina, I., Tárraga, J., Martínez, H., Barrachina, S., Castillo, M. I., Paschall, J., Salavert-Torres, J., Blanquer-Espert, I., Hernández-García, V., Quintana-Ortí, E. S., Dopazo, J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Full Papers
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833417/
https://www.ncbi.nlm.nih.gov/pubmed/26740642
http://dx.doi.org/10.1093/dnares/dsv039
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author Medina, I.
Tárraga, J.
Martínez, H.
Barrachina, S.
Castillo, M. I.
Paschall, J.
Salavert-Torres, J.
Blanquer-Espert, I.
Hernández-García, V.
Quintana-Ortí, E. S.
Dopazo, J.
author_facet Medina, I.
Tárraga, J.
Martínez, H.
Barrachina, S.
Castillo, M. I.
Paschall, J.
Salavert-Torres, J.
Blanquer-Espert, I.
Hernández-García, V.
Quintana-Ortí, E. S.
Dopazo, J.
author_sort Medina, I.
collection PubMed
description 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.
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spelling pubmed-48334172016-04-18 Highly sensitive and ultrafast read mapping for RNA-seq analysis Medina, I. Tárraga, J. Martínez, H. Barrachina, S. Castillo, M. I. Paschall, J. Salavert-Torres, J. Blanquer-Espert, I. Hernández-García, V. Quintana-Ortí, E. S. Dopazo, J. DNA Res Full Papers 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. Oxford University Press 2016-04 2016-01-05 /pmc/articles/PMC4833417/ /pubmed/26740642 http://dx.doi.org/10.1093/dnares/dsv039 Text en © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Full Papers
Medina, I.
Tárraga, J.
Martínez, H.
Barrachina, S.
Castillo, M. I.
Paschall, J.
Salavert-Torres, J.
Blanquer-Espert, I.
Hernández-García, V.
Quintana-Ortí, E. S.
Dopazo, J.
Highly sensitive and ultrafast read mapping for RNA-seq analysis
title Highly sensitive and ultrafast read mapping for RNA-seq analysis
title_full Highly sensitive and ultrafast read mapping for RNA-seq analysis
title_fullStr Highly sensitive and ultrafast read mapping for RNA-seq analysis
title_full_unstemmed Highly sensitive and ultrafast read mapping for RNA-seq analysis
title_short Highly sensitive and ultrafast read mapping for RNA-seq analysis
title_sort highly sensitive and ultrafast read mapping for rna-seq analysis
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833417/
https://www.ncbi.nlm.nih.gov/pubmed/26740642
http://dx.doi.org/10.1093/dnares/dsv039
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