Hardware Accelerated DNA Sequencing

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dc.contributor.advisorMagierowski, Sebastian
dc.creatorWu, Zhongpan
dc.date.accessioned2019-07-02T18:39:45Z
dc.date.available2019-07-02T18:39:45Z
dc.date.copyright2019-02-15
dc.date.issued2019-07-02
dc.date.updated2019-07-02T18:39:45Z
dc.degree.disciplineElectrical and Computer Engineering
dc.degree.levelMaster's
dc.degree.nameMASc - Master of Applied Science
dc.description.abstractDNA sequencing technology is quickly evolving. The latest developments ex- ploit nanopore sensing and microelectronics to realize real-time, hand-held devices. A critical limitation in these portable sequencing machines is the requirement of powerful data processing consoles, a need incompatible with portability and wide deployment. This thesis proposes a rst step towards addressing this problem, the construction of specialized computing modules { hardware accelerators { that can execute the required computations in real-time, within a small footprint, and at a fraction of the power needed by conventional computers. Such a hardware accel- erator, in FPGA form, is introduced and optimized specically for the basecalling function of the DNA sequencing pipeline. Key basecalling computations are identi- ed and ported to custom FPGA hardware. Remaining basecalling operations are maintained in a traditional CPU which maintains constant communications with its FPGA accelerator over the PCIe bus. Measured results demonstrated a 137X basecalling speed improvement over CPU-only methods while consuming 17X less power than a CPU-only method.
dc.identifier.urihttp://hdl.handle.net/10315/36356
dc.language.isoen
dc.rightsAuthor owns copyright, except where explicitly noted. Please contact the author directly with licensing requests.
dc.subjectBioinformatics
dc.subject.keywordsDNA Sequencing
dc.subject.keywordsNanopore
dc.subject.keywordsReal-time
dc.subject.keywordsHand-held
dc.subject.keywordsSequencing device
dc.subject.keywordsFPGA
dc.subject.keywordsHardware Accelerator
dc.subject.keywordsPCIe
dc.subject.keywordsCPU
dc.subject.keywordsBasecalling speed
dc.subject.keywordsPower Con- sumption
dc.titleHardware Accelerated DNA Sequencing
dc.typeElectronic Thesis or Dissertation

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