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dc.contributor.advisorAlkan, Can
dc.contributor.authorİçen, Balanur
dc.date.accessioned2019-10-10T06:36:09Z
dc.date.available2019-10-10T06:36:09Z
dc.date.copyright2019-09
dc.date.issued2019-10
dc.date.submitted2019-10-04
dc.identifier.urihttp://hdl.handle.net/11693/52537
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (M.S.): Bilkent University, Department of Computer Engineering, İhsan Doğramacı Bilkent University, 2019.en_US
dc.descriptionIncludes bibliographical references (leaves 38-45).en_US
dc.description.abstractGenomic variations that vary from single nucleotide polymorphisms (SNPs), small INDELs to structural variations (SVs) are discovered to have significant phenotypic effects on individuals. Among these genomic variations, SVs are changes that affect more than 50 nucleotides of DNA. SVs are linked to the sources of many genetic diseases such as autism, schizophrenia and chronic myelogenous leukemia. Accurate and precise characterization of these structural variants not only enables us to diagnose genetic diseases that are previously correlated with them but also it provides more reliable information to pursue higher levels of research in the genomic research pipelines. There are many SV detection tools that aim to find the approximate locations of SVs in genome, a further step in the pipeline is to refine those breakpoints of variants by a closer and more focused examination. By this means, genotyping step of structural variations would be faster using k-mer based alignment-free methods and more accurate since locations of SVs will be known with 1-5 base pair resolution compared to 300 - 500 base pair long confidence intervals. Moreover, further steps in the genomic pipelines based on the results of SV detection algorithms would have more definite data to build up on. In this thesis, we propose BROSV (Breakpoint Refinement of Structural Variation), a breakpoint refinement algorithm to obtain better resolution on SV breakpoints with split read analysis and local assembly methods using Illumina short reads and BWA alignment tool. Implementation is available at https://github.com/BilkentCompGen/brosv.en_US
dc.description.statementofresponsibilityby Balanur İçenen_US
dc.format.extentxii, 47 leaves : charts (some color) ; 30 cm.en_US
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectStructural variationen_US
dc.subjectBreakpoint refinementen_US
dc.subjectSplit readen_US
dc.titleBreakpoint refinement of genomic structural variation using split read analysisen_US
dc.title.alternativeAyrık okuma yöntemi ve yapısal varyasyonların kopma noktalarının rafine edilmesien_US
dc.typeThesisen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.publisherBilkent Universityen_US
dc.description.degreeM.S.en_US
dc.identifier.itemidB120113


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