Concurrent and Accurate Short Read Mapping on Multicore Processors
Scholar | Other documents of the author: Martínez Pérez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina Mir, Sergio; Castillo Catalán, Maribel; Dopazo, Joaquín; Quintana Ortí, Enrique S.
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TitleConcurrent and Accurate Short Read Mapping on Multicore Processors
We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA1, exploits a suffix array to ... [+]
We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA1, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100–400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR. [-]
Bibliographic citationMARTINEZ, Hector, et al. Concurrent and Accurate Short Read Mapping on Multicore Processors. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 2015, vol. 12, no 5, p. 995-1007.
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