次世代基因定序與生物資訊分析
Next-Generation Sequencing and Bioinformatics Analysis
| 節 | 週四 |
|---|---|
5 13:20–14:10 | 次世代基因定序與生物資訊分析 YD304 2 節連堂 |
6 14:20–15:10 |
* 根據陽明交大上課時間表所列
The objective of this course is to teach students comprehensive and practical knowledge of Illumina next-generation sequencing (NGS), ranging from sequencing technology, library preparation, and bioinformatics analysis. In the end of the course, students will be able to independently analyze Illumina sequencing data on organisms with reference genomes. 本課程的目標在於教導學生關於 Illumina 次世代基因定序之完整且實務的知識,包含定序技術、建庫實驗、以及生物資訊分析。修習完本課程之後,在具有參考基因體序列的前提下,學生將擁有獨立分析 Illumina 定序資料的能力。
- Basic understanding of molecular biology (e.g., DNA, RNA and PCR) is required. - Prior knowledge of Linux or any programming language is NOT required. - This course is taught in English. - 須具備基本的分生知識,例如 DNA、RNA、以及 PCR 的原理。 - 學生不需具備 Linux 或任何程式語言之基礎。 - 以英語授課為主。
Core concepts: 1. Illumina sequencing technology 2. Sequencing library preparation 3. Bioinformatics tools, algorithms, and file formats 4. Workshops: COVID-19 variant analysis - Bioinformatics analysis will be the major focus of this course, accounting for more than 75% of time. - Students will learn to conduct bioinformatics analysis in a Linux environment, via a series of workshops. - In our workshops, we analyze NGS data of COVID-19 and identify the variants. - Prior knowledge of Linux or any programming language is NOT required. - Basic understanding of molecular biology (e.g., DNA, RNA and PCR) is required. - A personal laptop is required. Windows, Mac, and Linux operating systems are all acceptable. - This course will be lectured mainly in English. Students are welcomed, but not required, to speak in English. - Due to time constraints, theoretical details of computational algorithms will not be covered in this course. 核心概念: 1. Illumina定序科技 2. 定序建庫實驗 3. 生物資訊工具、演算法、檔案格式 4. 工作坊:新冠病毒變種分析 - 生物資訊分析將是本課程之主軸,佔75%以上的授課時間。 - 學生將由工作坊的形式,實際設置Linux作業環境,並學習操作生物資訊分析軟體。 - 在工作坊中,我們將會分析新冠病毒的定序資料,確認變種株。 - 選修此課不需具備Linux或任何程式語言之基礎。 - 選修此課須具備基本的分生知識,例如DNA、RNA、以及PCR的原理。 - 需自備個人筆電。作業系統不限,Windows、Mac、或是Linux皆可。 - 主要以英語授課。學生可以中文問答討論。 - 由於時間限制,本課程將著重於實務知識,而不深入介紹各演算法之數學理論基礎。 相關學習網址: - Illumina Sequencing by Synthesis: https://www.youtube.com/watch?v=fCd6B5HRaZ8 - Beginner's Guide to the Bash Terminal: https://www.youtube.com/watch?v=oxuRxtrO2Ag - 10 Linux Terminal Commands for Beginners: https://www.youtube.com/watch?v=CpTfQ-q6MPU - 鳥哥的 Linux 私房菜: http://linux.vbird.org/ - Ben Langmead: https://www.youtube.com/user/BenLangmead - StatQuest with Josh Starmer: https://www.youtube.com/c/joshstarmer - Bioinformatics Algorithms: An Active Learning Approach: https://www.youtube.com/c/bioinfalgorithms
Midterm take-home exam (50%) & Final oral presentation (50%) 期中在家作業考試 (50%) & 期末口說報告 (50%)
| 週次 | 主題 |
|---|---|
| 第 1 週 | Greetings & Introduction 歡迎 & 簡介 |
| 第 2 週 | Overview of Illumina Sequencing Linux, Mac, Windows Subsystem for Linux Illumina 定序概述 作業系統簡介 |
| 第 3 週 | Illumina DNA Library Preparation Set up WSL 2 Illumina DNA 定序建庫 安裝設定 WSL 2 |
| 第 4 週 | RNA-seq Library Preparation Basic Linux Commands RNA 定序建庫 基本 Linux 指令 |
| 第 5 週 | Office Hour 問答時間 |
| 第 6 週 | Midterm Exam 期中考 |
| 第 7 週 | Overview of NGS Data-analysis Pipeline Anaconda Software Installation NGS 資料分析概述 Anaconda 軟體安裝 |
| 第 8 週 | Read Mapping Troubleshoot 序列回貼 疑難排除 |
| 第 9 週 | Variant Calling and Annotation (I) SARS-CoV-2 Read Mapping 變異偵測與註解 (I) SARS-CoV-2 序列回貼 |
| 第 10 週 | Variant Calling and Annotation (II) Integrative Genomics Viewer (IGV) 變異偵測與註解 (II) Integrative Genomics Viewer (IGV) |
| 第 11 週 | Enrichment Analysis (I) Troubleshoot 富集分析 (I) 疑難排除 |
| 第 12 週 | Enrichment Analysis (II) SARS-CoV-2 Variant Calling 富集分析 (II) SARS-CoV-2 變異偵測 |
| 第 13 週 | Genome Assembly and Annotation SARS-CoV-2 Variant Annotation 基因體序列重組與註解 SARS-CoV-2 變異註解 |
| 第 14 週 | Cloud Computing and Productionization Troubleshoot 雲端運算與軟體產品化 疑難排除 |
| 第 15 週 | Office Hour 問答時間 |
| 第 16 週 | Final Oral Presentation 期末口頭報告 |
| 第 17 週 | TBD 彈性教學 |
| 第 18 週 | TBD 彈性教學 |
- 聯絡方式
- ylin@nycu.edu.tw