• Anuncio de defensa de tesis doctoral

  • High-performance computing in bioinformatics: accelerating de novo assembly


    Doctoranda: Elena María Espinosa García

    Universidad: Universidad de Málaga

    Programa de doctorado: Tecnologías Informáticas

    Directores: Óscar Plata González y Rafael Larrosa Jiménez

    Tutor: Eladio Gutierrez Carrasco

    Fecha y hora de defensa: 2025-10-10 a las 10:40 horas

    Lugar: Sala de juntas de la ETS de Ingeniería de Telecomunicación

  • Summary: Advances in sequencing technologies have significantly improved the accuracy of genome assemblies and made the process more feasible. In parallel, new data structures, efficient algorithms, and computational techniques have been developed to address these challenges. Despite these improvements, de novo assembly still demands substantial computational resources, and remains an active area of research with ongoing development of diverse methods and strategies.

    In this thesis, we conduct an in-depth study of de novo genome assembly and its main bottlenecks. Building on these findings, we propose software- and hardware-level solutions to accelerate de novo genome assembly and make its computation as energy-efficient as possible. To this end, this work includes a comprehensive review of de novo genome assembly, a benchmark analysis of the most widely used assemblers to identify key bottlenecks, and the proposal of two acceleration tools: SeqMatcher and GenTEK.