NCHU Course Outline

Course Name	(中) 散彈槍定序原理與實習(5147)
	(Eng.) Shutgun Sequencing:Principle and Experiment
Offering Dept	Graduate Institute of Genomics and Bioinformatics
Course Type	Elective	Credits	2	Teacher	YING-TSONG CHEN
Department	Department of Life Sciences/Undergraduate	Language	English	Semester	2025-SPRING
Course Description	Shotgun Sequencing is a foundational technique in genomics research. It involves fragmenting the genome into smaller pieces for DNA sequencing, followed by assembling the sequenced fragments by overlapping reads to generate the complete genome sequence. This approach allows for rapid and efficient sequencing of entire genomes. Shotgun Sequencing is crucial for identifying genetic variations, studying genome structures, and discovering new genes. It forms the basis of modern precision medicine and finds extensive applications in the research of various organisms, including humans, animals, plants, and microorganisms. Content in brief: The course is conducted entirely in English (EMI). It covers the principles of various high-throughput genomic sequencing technologies, with a focus on Shotgun Sequencing strategies. Practical sessions include hands-on experience with Illumina short-read sequencing and Nanopore long-read sequencing. Genomic bioinformatics instruction covers Linux workstation usage, command-line interface operations, scripting languages (shell script/python), and progresses from basic to advanced genomic assembly analysis and visualization software package installation and usage. Bacterial Genome Project: The course revolves around a Bacterial Genome Project, allowing participants to engage in various aspects such as genome DNA purification, quality control, preparation of different sequencing libraries, hands-on high-throughput sequencing experiments, and learning sequential data processing, assembly, annotation, comparative genomics, database operations, and visualization analysis. Teaching Methods: The course employs a combination of classroom lectures (including multimedia presentations), laboratory sessions, and computer-based bioinformatics practical classes. The instructors, with over twenty years of experience in executing diverse genomics projects, emphasize strategic comparisons and considerations for different platforms within genomics projects. Practical problem-solving skills for various technical issues encountered in genomics projects are covered. Facility Visits: As a unique feature, the course includes planned visits to a core facility during the semester. Led by the course instructor, students will have the opportunity to visit high-throughput genomic facilities, including large Illumina sequencing platforms, traditional Sanger automated sequencing, or third-generation sequencing facilities.
Prerequisites				self-directed learning in the course	Y

Relevance of Course Objectives and Core Learning Outcomes(%)			Teaching and Assessment Methods for Course Objectives
Course Objectives	Competency Indicators	Ratio(%)	Teaching Methods	Assessment Methods
By the end of this course, students will be able to: Understand the principles and applications of Shotgun Sequencing and its role in modern genomics research. Gain hands-on experience with high-throughput sequencing technologies, including Illumina and Nanopore platforms, and understand their comparative strengths and limitations. Execute a complete bacterial genome project, encompassing DNA extraction, sequencing library preparation, data assembly, annotation, and comparative analysis. Develop bioinformatics skills, including command-line operations, scripting, and the use of advanced genomic analysis and visualization tools. Critically evaluate sequencing strategies and troubleshoot technical challenges in genomics projects. Apply genomic research techniques to broader contexts, such as identifying genetic variations, studying microbial diversity, and exploring applications in medicine and biotechnology.			topic Discussion/Production Visit Discussion Practicum Lecturing	Written Presentation Attendance Oral Presentation Internship
Course Content and Homework/Schedule/Tests Schedule
Week Course Content Week 1 Introduction Week 2 Sequencing Technologies Week 3 Experimental Design in Genomics Week 4 DNA Extraction and QC Week 5 Library preparation for Illumina Week 6 Library preparation for Nanopore Week 7 Sequencing Run and Facility Visit Week 8 Mid-term Week 9 Introduction to Linux for Bioinformatics Week 10 Read QC and trimming Week 11 Genome Assembly Week 12 Genome Annotation Week 13 Comparative Genomics Week 14 Visualization and Reporting Week 15 Case study in Genomics Week 16 Final Presentation Week 17 self-directed learning Week 18 self-directed learning
Evaluation
Participation, Discussion, Reports
Textbook & other References
Papers, Lab protocols, URL to the materials will be provided
Teaching Aids & Teacher's Website
Office Hours
Monday 9-12 AM Thursday 9-12AM, 14-16PM
Sustainable Development Goals, SDGs
include experience courses：N

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Update Date, year/month/day：2025/01/09 14:29:32	Printed Date, year/month/day：2025 / 1 / 22
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