An FPGA-based data pre-processing architecture to accelerate De-novo genome assemblyAn FPGA-based data pre-processing architecture to accelerate De-novo genome assembly Πλήρης Δημοσίευση σε Συνέδριο Conference Full Paper 2023-05-122021enThis work has been partially funded by the EU FP7 Project “QualiMaster - A Configurable Real-time Data Processing Infrastructure Mastering Autonomous Quality Adaptation”, Reference Number 619525, funded under the call FP7-ICT- 2013-1.Genome assembly is a field of bioinformatics which refers to the process of taking small fragments of genetic material and putting them back together in order to reconstruct the original DNA sequence from which the fragments originated. As the DNA genome assembly input datasets in most cases have a very large amount of data, it is important to develop custom architectures in order to speed up these processes and gain significant execution time reduction. In this paper we present the Reads Matching Filter (RMF), an input dataset prefiltering process, based on string matching and implemented on Field Programmable Gate Array (FPGA) technology, in order to reduce the genome assembly execution time. The outputs of the RMF running on the FPGA as well as the original input dataset are given as input to the Velvet genome assembler which produces the assembly of the input sequences. The Velvet genome assembler is based on the manipulation of de Bruijn graphs, and produces its output via the removal of errors and the simplication of repeated regions. The FPGA-based RMF pre-filtering process manages to speedup the entire genome assembly processing, including I/O, by up to 6 times, while maintaining the quality of the output sequence contigs (i.e. the series of overlapping DNA sequences).http://creativecommons.org/licenses/by/4.0/2021 IEEE 21st International Conference on Bioinformatics and Bioengineering Galanos Georgios Γαλανος Γεωργιος Malakonakis Pavlos Μαλακωνακης Παυλος Dollas Apostolos Δολλας Αποστολος Institute of Electrical and Electronics Engineers FPGA accelerator Genome assembly Dataset filtering Velvet de Bruijn graphs