Concurrent and Accurate RNA Sequencing on Multicore Platforms
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Altres documents de l'autoria: Martínez Pérez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Dopazo, Joaquín; Quintana-Orti, Enrique S.
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Concurrent and Accurate RNA Sequencing on Multicore PlatformsAutoria
Data de publicació
2013-04-02Editor
Departament d'Enginyeria i Ciència dels Computadors, Universitat Jaume ITipus de document
info:eu-repo/semantics/reportParaules clau / Matèries
Resum
In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers
equipped with multicore processors. Our software, named HPG-aligner1, leverages the speed of the Burrow ... [+]
In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers
equipped with multicore processors. Our software, named HPG-aligner1, leverages the speed of the Burrows-Wheeler
Transform to map a large number of RNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman
algorithm, that is employed to deal with conflictive reads. The aligner is complemented with a careful strategy to
detect splice junctions based on the division of RNA reads into short segments (or seeds), which are then mapped onto
a number of candidate alignment locations, providing useful information for the successful alignment of the complete
reads.
Experimental results on platforms with AMD and Intel multicore processors report the remarkable parallel performance
of HPG-aligner, on short and long RNA reads, which excels in both execution time and sensitivity to an
state-of-the-art aligner such as TopHat 2 built on top of Bowtie and Bowtie 2. [-]
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info:eu-repo/semantics/openAccess
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