Biomedical Sciences ETDs


Antoine Ho

Publication Date



The process of sequencing a genome involves many steps, and accordingly, this project contains work from each of those steps. Genome sequencing begins with acquisition of sequence data, therefore, a novel biochemistry was utilized and optimized for the Sequencing By Ligation (SBL) process. A cyclic SBL protocol was created that could be utilized to extend sequencing reads in both the 5' and 3' directions, for an increase in read length and thru-put. After sequence acquisition, there is the process of data analysis, and the focus shifted to creating software that could take sequence information and match up the individual reads to a reference genome with greater speed and efficiency than other commonly-used software. The Sequence Analysis Workbench Tool, SAWTooth, was written and shown to outperform contemporaries NOVOAlign and BOWTIE. Finally, the last aspect of genome sequencing is de novo assembly, prompting a comparative analysis of three assemblers: CLC Genomics Workbench, Velvet Assembler, and MIRA. Results were generated using Mauve to assess the general effects of different sequencing platforms on the final assembly.


Sequencing, Next-Generation, Analysis, Assembly, Sequencing By Ligation, Comparison

Document Type




Degree Name

Biomedical Sciences

Level of Degree


Department Name

Biomedical Sciences Graduate Program

First Committee Member (Chair)

Peabody, David

Second Committee Member

Werner-Washburne, Maggie