@article {1162,
	title = {Concurrent and Accurate Short Read Mapping on Multicore Processors.},
	journal = {IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM},
	volume = {12},
	year = {2015},
	month = {2015 Sep-Oct},
	pages = {995-1007},
	abstract = {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, [Formula: see text] ([Formula: see text] is an open-source application. The software is available at http://www.opencb.org, 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 [Formula: see text], 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.},
	keywords = {HPC, NGS, short real mapping},
	issn = {1557-9964},
	doi = {10.1109/TCBB.2015.2392077},
	url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=\&arnumber=7010005},
	author = {Martinez, Hector and T{\'a}rraga, Joaqu{\'\i}n and Medina, Ignacio and Barrachina, Sergio and Castillo, Maribel and Dopazo, Joaquin and Quintana-Orti, Enrique S}
}
@article {1076,
	title = {Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {30},
	year = {2014},
	month = {2014 Aug 20},
	pages = {3396-3398},
	abstract = {HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20x for long reads) and more sensitive (over 98\% in a wide range of read lengths) than the current, state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.},
	keywords = {NGS, short read mapping. HPC. suffix arrays},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btu553},
	url = {http://bioinformatics.oxfordjournals.org/content/early/2014/08/19/bioinformatics.btu553.long},
	author = {T{\'a}rraga, Joaqu{\'\i}n and Arnau, Vicente and Martinez, Hector and Moreno, Raul and Cazorla, Diego and Salavert-Torres, Jos{\'e} and Blanquer-Espert, Ignacio and Joaqu{\'\i}n Dopazo and Medina, Ignacio}
}
