Embedded CMOS Basecalling for Nanopore DNA Sequencing

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dc.contributor.advisorMagierowski, Sebastian
dc.contributor.advisorGhafar-Zadeh, Ebrahim
dc.creatorWang, Chengjie
dc.date.accessioned2017-07-27T12:42:35Z
dc.date.available2017-07-27T12:42:35Z
dc.date.copyright2016-12-06
dc.date.issued2017-07-27
dc.date.updated2017-07-27T12:42:34Z
dc.degree.disciplineComputer Engineering
dc.degree.levelMaster's
dc.degree.nameMASc - Master of Applied Science
dc.description.abstractDNA sequencing is undergoing a profound evolution into a mobile technology. Unfortunately the effort needed to process the data emerging from this new sequencing technology requires a compute power only available to traditional desktop or cloud-based machines. To empower the full potential of portable DNA solutions a means of efficiently carrying out their computing needs in an embedded format will certainly be required. This thesis presents the design of a custom fixed-point VLSI hardware implementation of an HMM-based multi-channel DNA sequence processor. A 4096 state (6-mer nanopore sensor) basecalling architecture is designed in a 32-nm CMOS technology with the ability to process 1 million DNA base pairs per second per channel. Over a 100 mm^2 silicon footprint the design could process the equivalent of one human genome every 30 seconds at a power consumption of around 5 W.
dc.identifier.urihttp://hdl.handle.net/10315/33468
dc.language.isoen
dc.rightsAuthor owns copyright, except where explicitly noted. Please contact the author directly with licensing requests.
dc.subjectBioinformatics
dc.subject.keywordsNanopore
dc.subject.keywordsASIC
dc.subject.keywordsInformation processing
dc.subject.keywordsBasecalling
dc.subject.keywordsBasecaller
dc.subject.keywordsFixed-point
dc.subject.keywordsMulti-channel
dc.titleEmbedded CMOS Basecalling for Nanopore DNA Sequencing
dc.typeElectronic Thesis or Dissertation

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