IMPROVING GENOME ASSEMBLY BY IDENTIFYING RELIABLE SEQUENCING DATA BY

ABSTRACT OF THE DISSERTATION Improving genome assembly by identifying reliable sequencing data by Rajat Shuvro Roy Dissertation Director: Alexander Schliep De novo Genome assembly and k-mer frequency counting are two of the classical prob-lems of Bioinformatics. k-mer counting helps to identify genomic k-mers from sequenced reads which may then inform read correction or genome assembly. Genome assembly has two major subproblems: contig construction and scaffolding. A contig is a continu-ous sub-sequence of the genome assembled from sequencing reads. Scaffolding attempts to construct a linear sequence of contigs (with possible gaps in between) using paired reads (two reads whose distance on the genome is approximately known). In this the-sis I will present a new computationally efficient tool for identifying frequent k-mers which are more likely to be genomic, and a set of linear inequalities which can improv