M.S. Thesis Defense: Richard Mwaba
June 22, 2022
11 a.m.–12 p.m.
Zoom: https://unl.zoom.us/j/99009366683
“ConSemblEX: A Consensus-Based Approach That Extends ConSemble and Improves Transcriptome Assembly”
An accurate transcriptome is essential to understanding biological systems enabling system-level analyses such as gene expression, gene discovery, and gene-regulatory network construction. However, assembling an accurate transcriptome is challenging, especially for organisms without adequate reference genomes or transcriptomes. Several methods for transcriptome assembly with different approaches exist. However, it is still difficult to establish the most accurate methods. This thesis explores the different transcriptome assembly methods and compares their performances using simulated benchmark transcriptomes with varying complexity. We also introduce ConSemblEX to improve a consensus-based ensemble transcriptome assembler, ConSemble, in three main areas; we provide the ability to use any number of assemblers, provide a variety of consensus assembly outputs and provide information about the effect of each assembler in the final assembly. Using five de novo assembly methods in ConSemblEX, we increased the assembly accuracy by 15% and assembled fewer contigs incorrectly. With five genome-guided assemblers, we increased the number of correctly assembled contigs by 10% while reducing the number of incorrectly assembled contigs. Thus, we demonstrated that we could further improve transcriptome assembly in both the de novo and genome-guided approaches by using more assembly methods and having more information about how the methods overlap.
Committee:
Dr. Jitender Deogun (Advisor)
Dr. Etsuko Moriyama (School of Biological Sciences)
Dr. Juan Cui