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 Advisor

Edwards, Jeremy S.

Second Advisor

Atlas, Susan R.

First Committee Member (Chair)

Peabody, David

Second Committee Member

Werner-Washburne, Maggie