Browsing by Author "Aguado Puig, Quim"

Now showing items 1-6 of 6

    • Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm 

      Aguado Puig, Quim; Marco-Sola, Santiago; Moure López, Juan Carlos; Castells Rufas, David; Álvarez Martí, Lluc; Espinosa Morales, Antonio; Moretó Planas, Miquel (Institute of Electrical and Electronics Engineers (IEEE), 2022-06-10)
      Article
      Open Access
      Sequence alignment remains a fundamental problem with practical applications ranging from pattern recognition to computational biology. Traditional algorithms based on dynamic programming are hard to parallelize, require ...

    • Accelerating pairwise sequence alignment on GPUs using the Wavefront Algorithm 

      Aguado Puig, Quim (Universitat Politècnica de Catalunya, 2022-10-19)
      Master thesis
      Open Access
      Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic ...

    • GenArchBench: A genomics benchmark suite for arm HPC processors 

      López Villellas, Lorien; Langarita Benítez, Rubén; Badouh, Asaf; Soria Pardos, Víctor; Aguado Puig, Quim; López Paradís, Guillem; Doblas Font, Max; Setoain, Javier; Kim, Chulho; Ono, Makoto; Armejach Sanosa, Adrià; Marco Sola, Santiago; Alastruey Benedé, Jesús; Ibáñez Marín, Pablo; Moretó Planas, Miquel (Elsevier, 2024-08)
      Article
      Open Access
      Arm usage has substantially grown in the High-Performance Computing (HPC) community. Japanese supercomputer Fugaku, powered by Arm-based A64FX processors, held the top position on the Top500 list between June 2020 and June ...

    • GMX: Instruction set extensions for fast, scalable, and efficient genome sequence alignment 

      Doblas Font, Max; Lostes Cazorla, Oscar; Aguado Puig, Quim; Cebry, Nicholas; Fontova Muste, Pau; Batten, Christopher; Marco Sola, Santiago; Moretó Planas, Miquel (Association for Computing Machinery (ACM), 2023)
      Conference report
      Open Access
      Sequence alignment remains a fundamental problem in computer science with practical applications ranging from pattern matching to computational biology. The ever-increasing volumes of genomic data produced by modern DNA ...

    • OpenCL-based FPGA accelerator for semi-global approximate string matching using diagonal bit-vectors 

      Castells Rufas, David; Marco-Sola, Santiago; Aguado Puig, Quim; Espinosa Morales, Antonio; Moure López, Juan Carlos; Alvarez Martí, Lluc; Moretó Planas, Miquel (Institute of Electrical and Electronics Engineers (IEEE), 2021)
      Conference report
      Open Access
      An FPGA accelerator for the computation of the semi-global Levenshtein distance between a pattern and a reference text is presented. The accelerator provides an important benefit to reduce the execution time of read-mappers ...

    • WFA-GPU: Gap-affine pairwise read-alignment using GPUs 

      Aguado Puig, Quim; Doblas Font, Max; Matzoros, Christos; Espinosa Morales, Antonio; Moure López, Juan Carlos; Marco-Sola, Santiago; Moretó Planas, Miquel (2023-12)
      Article
      Open Access
      Motivation: Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on ...