Genome scaffolding using poled clone sequencing

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buir.advisorAlkan, Can
dc.contributor.authorDal, Elif
dc.date.accessioned2016-01-08T20:18:23Z
dc.date.available2016-01-08T20:18:23Z
dc.date.issued2014
dc.departmentDepartment of Computer Engineeringen_US
dc.descriptionAnkara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2014.en_US
dc.descriptionThesis (Master's) -- Bilkent University, 2014.en_US
dc.descriptionIncludes bibliographical references leaves 49-53.en_US
dc.description.abstractThe DNA sequencing technologies hold great promise in generating information that will guide scientists to learn more about how the genome affects human health, organismal evolution, and genetic relationships between individuals of the same species. The process of generating raw genome sequence data becomes cheaper, faster, but more error prone. Assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ in terms of their performance, and in their final output. More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. In this thesis, we evaluated the accuracies of several genome scaffolding algorithms using two different types of data generated from the genome of the same human individual: i) whole genome shotgun sequencing (WGS), and ii) pooled clone sequencing (PCS). We observed that, it is possible to obtain less number of scaffolds with longer total assemble length if PCS data is used, compared to using only WGS data. However, the current scaffolding algorithms are developed only for WGS, and PCS-aware scaffolding algorithms remain an open problem.en_US
dc.description.degreeM.S.en_US
dc.description.statementofresponsibilityDal, Elifen_US
dc.embargo.release2016-12-29
dc.format.extentxii, 54 leaves, graphicsen_US
dc.identifier.itemidB149303
dc.identifier.urihttp://hdl.handle.net/11693/18338
dc.language.isoEnglishen_US
dc.publisherBilkent Universityen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectGenome Assembly and Scaffoldingen_US
dc.subjectHigh Throughput Sequencingen_US
dc.subjectPooled Clone Sequencingen_US
dc.subject.lccQH447 .D35 2014en_US
dc.subject.lcshGenomics.en_US
dc.subject.lcshHuman genome project.en_US
dc.subject.lcshMolecular genetics.en_US
dc.titleGenome scaffolding using poled clone sequencingen_US
dc.typeThesisen_US

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