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Institutional Repository [SANDBOX]
Technical University of Crete
Technical University of Crete
EN
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EL
| URI | http://purl.tuc.gr/dl/dias/EAB4F00F-749F-4529-96C2-7E4E9EB0057D | - |
| Identifier | https://doi.org/10.26233/heallink.tuc.91724 | - |
| Language | en | - |
| Extent | 95 pages | en |
| Extent | 1.1 megabytes | en |
| Title | FPGA-Based system design for applications of de Bruijn Graphs | en |
| Title | Σχεδίαση συστήματος βασισμένου σε αναδιατασσόμενη λογική για εφαρμογές γράφων de Bruijn | el |
| Creator | Rompogiannakis Emmanouil-Eleftherios | en |
| Creator | Ρομπογιαννακης Εμμανουηλ-Ελευθεριος | el |
| Contributor [Thesis Supervisor] | Dollas Apostolos | en |
| Contributor [Thesis Supervisor] | Δολλας Αποστολος | el |
| Contributor [Committee Member] | Ioannidis Sotirios | en |
| Contributor [Committee Member] | Ιωαννιδης Σωτηριος | el |
| Contributor [Committee Member] | Sotiriadis Evripidis | en |
| Contributor [Committee Member] | Σωτηριαδης Ευριπιδης | el |
| Publisher | Πολυτεχνείο Κρήτης | el |
| Publisher | Technical University of Crete | en |
| Academic Unit | Technical University of Crete::School of Electrical and Computer Engineering | en |
| Academic Unit | Πολυτεχνείο Κρήτης::Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών | el |
| Content Summary | The 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 Item | Διπλωματική Εργασία | el |
| Type of Item | Diploma Work | en |
| License | http://creativecommons.org/licenses/by/4.0/ | en |
| Date of Item | 2022-03-08 | - |
| Date of Publication | 2022 | - |
| Subject | De Bruijn Graph | en |
| Subject | de Novo genome assembly | en |
| Bibliographic Citation | Emmanouil-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, 2022 | en |
| Bibliographic Citation | Εμμανουήλ-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, 2022 | el |
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