Browsing by Author "f3dfba9a-c77d-4efa-ba0d-e6460424356a"
Now showing items 1-7 of 7
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A framework for genomic sequencing on clusters of multicore and manycore processors
Martínez Pérez, Héctor; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Tárraga, Joaquín; Medina, Ignacio; Dopazo, Joaquín; Quintana-Orti, Enrique S. Sage (2016-06)The advances in genomic sequencing during the past few years have motivated the development of fast and reliable software for DNA/RNA sequencing on current high performance architectures. Most of these efforts target ... -
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
Tárraga, Joaquín; Arnau, Vicente; Martínez Pérez, Héctor; Moreno, Raul; Cazorla, Diego; Salavert Torres, José; Blanquer Espert, Ignacio; Dopazo, Joaquín; Medina, Ignacio Oxford University Press (2014-08)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 ... -
Concurrent and Accurate RNA Sequencing on Multicore Platforms
Martínez Pérez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Dopazo, Joaquín; Quintana-Orti, Enrique S. Departament d'Enginyeria i Ciència dels Computadors, Universitat Jaume I (2013-04-02)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-aligner1, leverages the speed of the Burrows-Whe ... -
Concurrent and Accurate Short Read Mapping on Multicore Processors
Martínez Pérez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Dopazo, Joaquín; Quintana-Orti, Enrique S. IEEE (2015-09)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 ... -
Dynamic reconfiguration of noniterative scientific applications A case study with HPG aligner
Iserte, Sergio; Martínez Pérez, Héctor; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Mayo, Rafael; Peña Monferrer, Antonio J. Springer (2018-09)Several studies have proved the benefits of job malleability, that is, the capacity of an application to adapt its parallelism to a dynamically changing number of allocated processors. The most remarkable advantages of ... -
FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters
Martínez Pérez, Héctor; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Quintana-Orti, Enrique S.; Rambla, Jordi; Farré, Xavier; Navarro, Arcadi Mary Ann Liebert (2018-08)We introduce a version of the epistasis test in FaST-LMM for clusters of multithreaded processors. This new software maintains the sensitivity of the original FaST-LMM while delivering acceleration that is close to linear ... -
Highly sensitive and ultrafast read mapping for RNA-seq analysis
Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Martínez Pérez, Héctor; Medina, Ignacio; Tárraga, Joaquín; Quintana-Orti, Enrique S.; Dopazo, Joaquín; Salavert Torres, José; Blanquer Espert, Ignacio; Paschall, J.; Hernández-García, V. Oxford University Press (2016)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 ...