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
