Date of Graduation

5-2021

Document Type

Thesis

Degree Name

Bachelor of Science in Computer Engineering

Department

Computer Science and Computer Engineering

Advisor/Mentor

Thompson, Dale

Committee Member/Reader

Steven, Ricke

Committee Member/Second Reader

Patitz, Matthew

Abstract

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after importing and demultiplexing sequences in the Qiime2 pipeline. By automating this process and removing the need for manual interaction by the researcher, this plugin provides another opportunity to automate another standard bioinformatic analysis procedure.

Keywords

Qiime2, Bioinformatics, Microbiome, TruncTrimmer

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