A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

Abstract

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21st century STEM workforce. Recent evidence however demonstrates that there are significant barriers to teaching these skills at the undergraduate level including lack of faculty training, lack of student interest in bioinformatics, lack of vetted teaching materials, and overly full curricula. To this end, the James Madison University, Center for Genome & Metagenome Studies (JMU CGEMS) and other PUI collaborators are devoted to developing and disseminating engaging bioinformatics teaching materials specifically designed for streamlined integration into general undergraduate biology curriculum. Here, we have developed and integrated a fun introductory level lesson to command line next generation sequencing (NGS) analysis into a large enrollment core biology course. This one-off activity takes a crucial but mundane aspect of NGS quality control (QC) analysis and incorporates the use of Emoji data outputs using the software FASTQE to pique student interest. This amusing command line analysis is subsequently paired with a more rigorous research-grade software package called FASTP in which students complete sequence QC and filtering using a few simple commands. Collectively, this short lesson provides novice-level faculty and students an engaging entry point to learning basic genomics command line programming skills as a gateway to more complex and elaborated applications of computational bioinformatics analyses. Citation: St. Jacques RM, Maza WM, Robertson SD, Lonsdale A, Murray CS, Williams JJ, Enke RA. 2021. A fun introductory command line lesson: Next generation sequencing quality analysis with Emoji! CourseSource. https://doi.org/10.24918/cs.2021.17 Editor: Srebrenka Robic, Agnes Scott College Received: 8/22/2019; Accepted: 2/24/2021; Published: 4/13/2021 Copyright: © 2021 St. Jacques, Maza, Robertson, Lonsdale, Murray, Williams, and Enke. This is an open-access article distributed under the terms of the Creative Commons AttributionNonCommercial-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: None of the authors has a financial, personal, or professional conflict of interest related to this work. This work was supported by James Madison University 4-VA funding as well as National Science Foundation, Improving Undergraduate STEM Education Grant #1821657 awarded to R.A.E and the JMU College of Science and Mathematics. Supporting Materials: Supporting Files S1. FASTQE – Pre-class assignment; S2. FASTQE – Male5-oral1.fastq file; S3. FASTQE – Male5-oral2.fastq file; S4. FASTQE – Female2-oral1.fastq file; S5. FASTQE – Lecture slides; S6. FASTQE – Jupyter Notebook alternative implementation instructions; S7. FASTQE – Instructor version of lesson; and S8. FASTQE – Student version of lesson. *Correspondence to: Ray Enke, Department of Biology, James Madison University, Harrisonburg, VA, USA. Email: enkera@jmu.edu CourseSource | www.coursesource.org 2021 | Volume 08 1 Lesson