Physical Sciences and Mathematics Commons^™

Metagenome Assembly, Wenjing Wan

Electronic Thesis and Dissertation Repository

The advent of the next generation sequencing technology (NGS) makes it possible to study metagenomics data which is directly extracted and cloned from assemblage of micro-organisms. Metagenomics data are diverse in species and abundance. Because most genome assemblers are designed for single genome assembly, they could not perform well on metagenomics data. To deal with the mixed and not uniformly distributed metagenomics reads, we developed a novel metagenomic assembler named MetaSAGE, on the platform of the existing SAGE assembler. MetaSAGE finds contigs from the overlap graph based on the minimum cost flow theory and uses mate-pair information to extract scaffolds …

Error Correction In Next Generation Dna Sequencing Data, Michael Z. Molnar

Electronic Thesis and Dissertation Repository

Motivation: High throughput Next Generation Sequencing (NGS) technologies can sequence the genome of a species quickly and cheaply. Errors that are introduced by NGS technologies limit the full potential of the applications that rely on their data. Current techniques used to correct these errors are not sufficient, and a more efficient and accurate program is needed to correct errors.

Results: We have designed and implemented RACER (Rapid Accurate Correction of Errors in Reads), an error correction program that targets the Illumina genome sequencer, which is currently the dominant NGS technology. RACER combines advanced data structures with an intricate analysis of …

A New Algorithm For De Novo Genome Assembly, Md. Bahlul Haider

Electronic Thesis and Dissertation Repository

The enormous amount of short reads produced by next generation sequencing (NGS) techniques such as Roche/454, Illumina/Solexa and SOLiD sequencing opened the possibility of de novo genome assembly. Some of the de novo genome assemblers (e.g., Edena, SGA) use an overlap graph approach to assemble a genome, while others (e.g., ABySS and SOAPdenovo) use a de Bruijn graph approach. Currently, the approaches based on the de Bruijn graph are the most successful, yet their performance is far from being able to assemble entire genomic sequences. We developed a new overlap graph based genome assembler called Paired-End Genome ASsembly Using Short-sequences …