Concurrent and Accurate RNA Sequencing on Multicore Platforms

Concurrent and Accurate RNA Sequencing on Multicore Platforms
Héctor Martínez (1), Joaquín Tárraga (2), Ignacio Medina (2), Sergio Barrachina (1), Maribel Castillo (1), Joaquín Dopazo (2), Enrique S. Quintana-Ortí (1) ((1) Dpto. de Ingeniería y Ciencia de los Computadores, Universidad Jaume I, Castellón, Spain, (2) Computational Genomics Institute, Centro de Investigación Príncipe Felipe, Valencia, Spain)
(Submitted on 2 Apr 2013)

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-Aligner, 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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