Addressing the Black Box phenomenon of genome sequencing and assembly

Author

Brandon Carter, James Madison UniversityFollow

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Date of Graduation

Spring 2015

Document Type

Thesis

Degree Name

Bachelor of Science (BS)

Department

Department of Integrated Science and Technology

Advisor(s)

Louise Temple

Abstract

Genomics, a study of all genetic material in an organism, is a new discipline having a great impact on medicine, agriculture, and environmental phenomena. Most undergraduate faculty members were not formally trained in genomics and must retool themselves in order to stay current with these evolving technologies. Advances in sequencing technology have resulted in an explosion of “big data” that can only be managed and analyzed using digital methods. Multiple complex computer programs are required to teach students the concepts using hands-on methods. These programs are challenging to use, especially since the same faculty members lacking genomics training were not trained in computer science, either. The Howard Hughes Medical Institute set out to provide large numbers of faculty members and students with the opportunity to isolate viruses that infect bacteria (bacteriophages) and perform genetic analyses of these new viruses. This SEA-PHAGES education program has the mission to promote research in the field of bacteriophage genomics while training undergraduate students in original research. Although training for the discovery lab and genomics is provided, there is an area in the genomics analysis that is missing from this training, and this represents a lost opportunity for faculty members to teach the entire process of genomic analysis to their students. The goal of this work was to ameliorate this deficit by creating a manual that addresses one of the most difficult aspects of genomics analysis, assembly of DNA sequencing reads that are produced by modern sequencing equipment. In order to determine the interest in such a manual and assess the content to be included in the manual, SEA-PHAGES faculty members were surveyed at 87 universities involved in teaching the SEA-PHAGES viral discovery course. Of those surveyed, 39 faculty members responded, and the responses were used to guide the development of the manual. The 3 manual contains procedures necessary to assemble DNA and analyze the assembled output in a manner accessible to both faculty members and students. It guides the user from handling the raw sequence data through fully assembled viral genomes ready for genetic analysis, thus illuminating the “black box” phenomenon. The manual was piloted in two genomics courses at James Madison University and by multiple professors at other SEA-PHAGES member universities. The responses have been used to make improvements in the manual. The findings from this pilot test indicate that the manual was an effective tool for science professors and their students. The manual will be distributed freely and made available to researchers associated with the SEA-PHAGES consortium.

Recommended Citation

Carter, Brandon, "Addressing the Black Box phenomenon of genome sequencing and assembly" (2015). Senior Honors Projects, 2010-2019. 34.
https://commons.lib.jmu.edu/honors201019/34