An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching

Advances in Next Generation Sequencing (NGS) technology have led to development of many research methods for analyzing genomic data. Students studying biology at the undergraduate level must hone their skills at genomic analysis to participate in productive research during and after their undergraduate studies. To counteract the barriers such as a lack of funding, equipment, or bioinformatics experience at many undergraduate institutions, the GCAT-SEEK network has produced a tutorial designed to train biology and related majors about tools used for contemporary eukaryotic genomic analysis. This lesson allows students to work through relevant chapters including, but not limited to, quality filtering and trimming of short sequence reads, genome assembly, annotation, variant detection and genome visualization, with an emphasis on the Linux operating system. The tutorial has been used in a variety of settings including a completely independent self-paced tutorial for research students, a partially independent “flipped” classroom, a heavily supported semester-long laboratory, and as the basis for an 18-hour faculty-development workshop. After completion of these lessons, students should be able to demonstrate skills related to bioinformatics in the context of genomic data, as well as understand biological concepts involved in data quality, genome assembly, annotation and variant detection. Citation: Buonaccorsi, V.P., Hamlin, D. , Fowler, B. , Sullivan, C. , and Sickler, A. 2017. An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2017. 1 Editor: Kristin Fox, Union College, Schenectady, NY Received: 07/25/2016; Accepted: 11/04/2016; Published: 03/13/2017 Copyright: © 2017 Buonaccorsi, Hamlin, Fowler, Sullivan, and Sickler. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict of Interest and Funding Statement: This work was funded by the National Science Foundation (DBI-1248096), and a grant to Juniata College from the Howard Hughes Medical Institute through the Precollege and Undergraduate Science Education Program. There are no potential conflicts of interest Supporting Materials: S1. Eukaryotic Genome Analysis-Seven tutorial chapters, covering assembly, annotation, and variant discovery, S2. Eukaryotic Genome Analysis-Three pre-tutorial chapters, covering topics in basic Linux, relevant molecular biology, and genome biology, S3. Eukaryotic Genome Analysis-Quizzes accompanying pre-tutorial and tutorial chapters, S4. Eukaryotic Genome Analysis-Data directories accompanying tutorial chapters needed to complete each tutorial chapter, S5a. Eukaryotic Genome Analysis-Answers to pre-tutorial and tutorial chapter questions, S5b. Eukaryotic Genome Analysis-Answers to pre-tutorial and tutorial chapter questions, and S6. Eukaryotic Genome Analysis-Completed Linux directories for all tutorials. *Correspondence to: Department of Biology, 1700 Moore St, Huntingdon, PA, 16652 Email: buonaccorsi@juniata.edu CourseSource | www.coursesource. org 2017 | Volume 04 1 Lesson