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Designing a hardware accelerator for a selective sweep detection algorithm using high-level synthesis

Sterenborg, Niek (2021) Designing a hardware accelerator for a selective sweep detection algorithm using high-level synthesis.

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Abstract:Genetic analysis is used widely by humanity. Use cases range from researching adaptive evolution to combating drug resistance among diseases. Since natural selection was discovered humans have been developing their understanding of genetic phenomena continuously. Detecting selective sweeps can give insight in mutations of a species or population and help to take action if required. To detect these sweeps, some software solutions exist that use the sweep signatures around a selective sweep to determine the position of the sweep. In this paper the OmegaPlus algorithm is analyzed and accelerated with an FPGA. The core calculation of OmegaPlus is changed slightly so that it is suitable to be synthesized to HDL. Vivado High Level Synthesis is used to synthesize the code to HDL. OmegaPlus already has different versions that use multithreading to improve computation times. The throughput of these different versions is measured and compared with the throughput of the accelerator presented in this paper. The designed accelerator achieves speedups between 2.12x and 46.84x based on the version of OmegaPlus and the target FPGA
Item Type:Essay (Bachelor)
Faculty:EEMCS: Electrical Engineering, Mathematics and Computer Science
Subject:42 biology, 53 electrotechnology, 54 computer science
Programme:Electrical Engineering BSc (56953)
Link to this item:http://purl.utwente.nl/essays/87831
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