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dc.contributor.authorGoodarzi, Mohammad
dc.date.accessioned2014-02-25T21:22:52Z
dc.date.available2014-02-25T21:22:52Z
dc.date.issued2014-02-25
dc.identifier.urihttp://hdl.handle.net/10464/5235
dc.description.abstractDNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.en_US
dc.language.isoengen_US
dc.publisherBrock Universityen_US
dc.subjectDNA Assembly Problemen_US
dc.subjectde-novoen_US
dc.subjectContig Creation Algorithmen_US
dc.subjectBioinformaticsen_US
dc.titleNew Contig Creation Algorithm for the de novo DNA Assembly Problemen_US
dc.typeElectronic Thesis or Dissertationen_US
dc.degree.nameM.Sc. Computer Scienceen_US
dc.degree.levelMastersen_US
dc.contributor.departmentDepartment of Computer Scienceen_US
dc.degree.disciplineFaculty of Mathematics and Scienceen_US
dc.embargo.termsNoneen_US
refterms.dateFOA2021-08-02T01:52:28Z


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