• openAccess   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 ...
    • closedAccess   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 ...
    • openAccess   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 ...
    • openAccess   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 ...
    • openAccess   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 ...