University of Twente Student Theses


Performance of Smith-Waterman DNA sequence matching on a FPGA

Kingma, P.J. (2022) Performance of Smith-Waterman DNA sequence matching on a FPGA.

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Abstract:Because of advancements in molecular sequencing technology, a need for even faster processing of this fast-growing pool of data is needed. Preferably, this data is processed as vsoon as possible, as fast as possible, so having a low latency and high throughput is of importance. This usually includes finding matches between certain DNA sequences. These algorithms have a lot of parallelizable operations, and could have significant improvements in latency and throughput when implemented on a FPGA. One such algorithm is Smith-Waterman, which locates the best local alignment according to the set scoring system. The goal of this paper is to explore what the limits of current implementations of Smith-Waterman are, and how these limits show in the performance metrics of the algorithm’s hardware implementation.
Item Type:Essay (Bachelor)
Faculty:EEMCS: Electrical Engineering, Mathematics and Computer Science
Subject:53 electrotechnology
Programme:Electrical Engineering BSc (56953)
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