A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!-猫眼课题宝

DOI：

10.24918/cs.2021.17

发表时间：

2021-08

期刊：

CourseSource

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

R. Jacques;William M. Maza;Sabrina D. Robertson;Andrew Lonsdale;Caylin S. Murray;Jason J. Williams

在过去的十年中，DNA测序技术的根本性创新已经在21世纪世纪STEM劳动力中创造了对计算生物信息学分析的需求。然而，最近的证据表明，在本科阶段教授这些技能存在重大障碍，包括缺乏教师培训，学生对生物信息学缺乏兴趣，缺乏经过审查的教材，以及课程过于完整。为此，詹姆斯麦迪逊大学、基因组和元基因组研究中心（JMU CGEMS）和其他PUI合作者致力于开发和传播引人入胜的生物信息学教材，专门设计用于简化整合到普通本科生物学课程中。在这里，我们已经开发并集成了一个有趣的入门级课程，命令行下一代测序（NGS）分析到一个大的招生核心生物学课程。这个一次性的活动采取了NGS质量控制（QC）分析的一个重要但平凡的方面，并结合了使用FASTQE软件输出的数据，以激发学生的兴趣。这种有趣的命令行分析随后与更严格的研究级软件包FASTP配对，在该软件包中，学生使用一些简单的命令完成序列QC和过滤。总的来说，这个简短的课程为新手级教师和学生提供了一个学习基本基因组学命令行编程技能的切入点，作为计算生物信息学分析的更复杂和详细应用的门户。引文：圣雅克RM，马扎WM，罗伯逊SD，朗斯代尔A，默里CS，威廉姆斯JJ，恩克RA。2021.一个有趣的命令行入门课程：使用Jumeji进行下一代测序质量分析！CourseSource. https://doi.org/10.24918/cs.2021.17 编辑：Srebrenka Robic，Agnes Scott College接收：8/22/2019;接受：2/24/2021;出版：4/13/2021版权所有：© 2021 St. Jacques，Maza，Robertson，Lonsdale，Murray，威廉姆斯和Enke。这是一篇开放获取的文章，根据知识共享署名-非商业性-相同方式共享4.0国际许可证的条款分发，该许可证允许在任何媒体上不受限制的非商业性使用，分发和复制，前提是原作者和来源被记入。利益冲突和资金声明：没有作者有一个财务，个人或专业利益冲突与这项工作有关。这项工作得到了詹姆斯麦迪逊大学4-VA资金以及国家科学基金会的支持，提高本科生STEM教育补助金#1821657授予R.A.E和JMU科学与数学学院。支持材料：支持文件S1。FASTQE -课前作业; S2。FASTQE -Male 5-oral1.fastq文件; S3. FASTQE -Male 5-oral2.fastq文件; S4. FASTQE -Female 2-oral1.fastq文件; S5. FASTQE -讲座幻灯片; S6。FASTQE -笔记本替代实施说明; S7。FASTQE -课程的教师版本;和S8。FASTQE -学生版本的课程。* 通讯作者：Ray Enke，美国弗吉尼亚州哈里森堡詹姆斯麦迪逊大学生物系。电子邮件：enkera@jmu.edu CourseSource|www.coursesource.org 2021|第08卷第1课

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

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

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