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Title: | EVALUATION AND IMPROVEMENT OF GENOME ASSEMBLY | Authors: | XIE LUYU | ORCID iD: | orcid.org/0000-0003-3300-6401 | Keywords: | next-generation sequencing, genome assembly | Issue Date: | 23-Aug-2019 | Citation: | XIE LUYU (2019-08-23). EVALUATION AND IMPROVEMENT OF GENOME ASSEMBLY. ScholarBank@NUS Repository. | Abstract: | As a basic application of next-generation sequencing, genomic de novo assembly has benefited from the development of many assemblers. During a comparison between assemblies, it was found that existing metrics only provided limited insight on specific aspects of genome assembly quality, and sometimes even disagreed with each other. For better integrative comparison between assemblies, I propose a new genome assembly metric, PDR. It derives from a common question in genetic studies and takes completeness, contiguity, and correctness into consideration. Beyond assemblers, many assembly strategies were also developed. Among these strategies, the genetic map is the most widely adopted one in breeding studies. But genetic map construction requires numerous computational resources and underperforms when draft assembly contains misassembly. To address these limitations, I propose a new assembly-improving method, CAST. It first splits the draft assembly at genetically incoherent positions and then scaffolds contigs at genetically coherent positions. | URI: | https://scholarbank.nus.edu.sg/handle/10635/166270 |
Appears in Collections: | Ph.D Theses (Open) |
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