FPGA-Based system design for applications of de Bruijn GraphsFPGA-Based system design for applications of de Bruijn GraphsΣχεδίαση συστήματος βασισμένου σε αναδιατασσόμενη λογική για εφαρμογές γράφων de Bruijn Διπλωματική Εργασία Diploma Work 2022-03-082022enDe Bruijn GraphsThe mathematical properties of De Bruijn graph were originally introduced in 1951 by the Dutch mathematicians Tanja van Aardenne-Ehrenfests and Nicolaas Govert de Bruijn. The De Bruijn graph is a directed graph representing overlaps between sequences of symbols; it has several uses in the field of telecommunications in protocols and networks and in the field of Bioinformatics, specifically in De novo genome assembly. The properties of De Bruijn graph and its promising uses in De novo genome assembly have been presented in several scientific articles. In this thesis we have implemented an FPGA-based prototype hardware system for de Bruijn graph applications in de Novo genome assembly. We used the Russian genome assembler named SPAdes13.0 as a case study for the use of de Bruijn Graphs. The SPAdes.13.0 genome assembler is a current-generation tool, and it is widely used in the field. The SPAdes.13.0 is also used for the verification of our experimental results. The data sets used in this thesis come from to European Nucleotide Archive (ENA) . The FPGA Alveo U50 has been used as the target technology for experimental results in this thesis. The resulting speedup is modest (up to 1.14x-1.35x) for small data sets and the system has worse performance than SPAdes for large data sets, the bottleneck being the resources and the memory subsystem. Different accelerator cards with more storage capacity and resources could better exploit parallelism with more compute units. Thus, this thesis is more of a firstgeneration feasibility study, and can form the baseline for future accelerator architectures.http://creativecommons.org/licenses/by/4.0/Πολυτεχνείο Κρήτης::Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών ΥπολογιστώνRompogiannakis_Emmanouil-Eleftherios_Dip_2022.pdfChania [Greece]Library of TUC2022-03-08application/pdf1.1 MBfree Rompogiannakis Emmanouil-Eleftherios Ρομπογιαννακης Εμμανουηλ-Ελευθεριος Dollas Apostolos Δολλας Αποστολος Ioannidis Sotirios Ιωαννιδης Σωτηριος Sotiriadis Evripidis Σωτηριαδης Ευριπιδης Πολυτεχνείο Κρήτης Technical University of Crete De Bruijn Graph de Novo genome assembly