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FPGA-Based system design for applications of de Bruijn Graphs

Rompogiannakis Emmanouil-Eleftherios

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URIhttp://purl.tuc.gr/dl/dias/EAB4F00F-749F-4529-96C2-7E4E9EB0057D-
Identifierhttps://doi.org/10.26233/heallink.tuc.91724-
Languageen-
Extent95 pagesen
Extent1.1 megabytesen
TitleFPGA-Based system design for applications of de Bruijn Graphsen
TitleΣχεδίαση συστήματος βασισμένου σε αναδιατασσόμενη λογική για εφαρμογές γράφων de Bruijnel
CreatorRompogiannakis Emmanouil-Eleftheriosen
CreatorΡομπογιαννακης Εμμανουηλ-Ελευθεριοςel
Contributor [Thesis Supervisor]Dollas Apostolosen
Contributor [Thesis Supervisor]Δολλας Αποστολοςel
Contributor [Committee Member]Ioannidis Sotiriosen
Contributor [Committee Member]Ιωαννιδης Σωτηριοςel
Contributor [Committee Member]Sotiriadis Evripidisen
Contributor [Committee Member]Σωτηριαδης Ευριπιδηςel
PublisherΠολυτεχνείο Κρήτηςel
PublisherTechnical University of Creteen
Academic UnitTechnical University of Crete::School of Electrical and Computer Engineeringen
Academic UnitΠολυτεχνείο Κρήτης::Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστώνel
Content SummaryThe 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.en
Type of ItemΔιπλωματική Εργασίαel
Type of ItemDiploma Worken
Licensehttp://creativecommons.org/licenses/by/4.0/en
Date of Item2022-03-08-
Date of Publication2022-
SubjectDe Bruijn Graphen
Subjectde Novo genome assemblyen
Bibliographic CitationEmmanouil-Eleftherios Rompogiannakis, "FPGA-Based system design for applications of de Bruijn Graphs", Diploma Work, School of Electrical and Computer Engineering, Technical University of Crete, Chania, Greece, 2022en
Bibliographic CitationΕμμανουήλ-Ελευθέριος Ρομπογιαννάκης, "Σχεδίαση συστήματος βασισμένου σε αναδιατασσόμενη λογική για εφαρμογές γράφων de Bruijn", Διπλωματική Εργασία, Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, Πολυτεχνείο Κρήτης, Χανιά, Ελλάς, 2022el

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