@article {7,
	title = {Highly sensitive and ultrafast read mapping for RNA-seq analysis.},
	journal = {DNA Res},
	year = {2016},
	month = {2016 Jan 5},
	abstract = {<p>As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available.</p>},
	issn = {1756-1663},
	doi = {10.1093/dnares/dsv039},
	author = {Medina, I and T{\'a}rraga, J and Mart{\'\i}nez, H and Barrachina, S and Castillo, M I and Paschall, J and Salavert-Torres, J and Blanquer-Espert, I and Hern{\'a}ndez-Garc{\'\i}a, V and Quintana-Ort{\'\i}, E S and Dopazo, J}
}
@article {10,
	title = {Concurrent and Accurate Short Read Mapping on Multicore Processors.},
	journal = {IEEE/ACM Trans Comput Biol Bioinform},
	volume = {12},
	year = {2015},
	month = {2015 Sep-Oct},
	pages = {995-1007},
	abstract = {<p>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 SA (HPG Aligner SA 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 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.</p>},
	issn = {1557-9964},
	doi = {10.1109/TCBB.2015.2392077},
	author = {Mart{\'\i}nez, H{\'e}ctor and Tarraga, Joaquin and Medina, Ignacio and Barrachina, Sergio and Castillo, Maribel and Dopazo, Joaqu{\'\i}n and Quintana-Ort{\'\i}, Enrique S}
}
