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所在平台: Coursera |
课程主页: https://www.coursera.org/learn/wgs-bacteria
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课程名称：细菌基因组的全基因组测序 - 工具与应用 课程概述： 本课程将探讨细菌全基因组测序（WGS）的主题，该技术在医学领域的相关性日益增加。WGS技术及其应用在国际政治议程中占据重要位置，传统方法正被WGS技术取代，因此生物信息学工具在这个领域至关重要，帮助从业人员分析数据并获得可用于不同目的的结果。课程将使学习者理解WGS在细菌监测中的应用，包括物种识别、分型、抗生素抵抗和毒力特征的特征化以及质粒特征化。学习者将有机会通过在线工具的演示学习这些工具的用途，并通过使用可自由获得的WGS分析工具解决练习。 课程目标： 完成本课程后，您应能够： 1. 描述细菌分型的一般原则。 2. 举例说明全基因组测序在细菌病原体监测和抗生素抵抗方面的应用。 3. 应用基因组工具进行分型和监测。 4. 定义下一代测序的概念，并描述NGS的测序数据。 5. 描述如何从原始读取进行de novo组装到contigs。 6. 列举用于物种识别、MLST分型和抗性基因检测工具的原理。 7. 在其他细菌和病原体基因组的实际案例中应用物种识别、MLST分型和抗性基因检测工具。 8. 描述对沙门氏菌和大肠杆菌分型、质粒复制子检测和质粒分型工具的原理。 9. 在其他细菌和病原体基因组的实际案例中利用沙门氏菌和大肠杆菌分型、质粒复制子检测和质粒分型工具。 10. 解释并能够使用集成细菌分析管道进行基因组数据的批量分析和分型。 11. 演示如何基于SNP构建系统发育树。 12. 应用系统发育工具构建系统发育树并解释细菌或病原体菌株的关系。 13. 描述如何创建自己的序列数据库。 14. 利用MyDbFinder工具从全基因组测序中检测感兴趣的遗传标记。 课程大纲： - 模块1：细菌分型及全基因组测序在细菌病原体监测和抗生素抵抗中的应用简介。 - 模块2：下一代测序概论。 - 模块3：全基因组测序工具 - 物种识别、MLST分型和寻找抗性基因分析工具的演示。 - 模块4：全基因组测序工具 - 沙门氏菌和大肠杆菌分型及寻找质粒复制子的分析工具演示。 - 模块5：全基因组测序工具 - 多重分析、系统发育树构建以及从自制数据库寻找遗传标记的分析工具演示及总结性教程练习。
Name:Module 1
Description:Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to surveillance of bacterial pathogens and antimicrobial resistance
Name:Module 2
Description:Introduction to Next Generation sequencing
Name:Module 3
Description:Whole genome sequencing tools- demonstration of analysis tools for species identification, MLST typing and finding resistance genes
Name:Module 4
Description:Whole genome sequencing tools- demonstration of analysis tools for Serotyping of Salmonella and Escherichia coli strains , and finding plasmid replicons
Name:Module 5
Description:Whole genome sequencing tools- demonstration of analysis tools for multiple analyzes, phylogenetic tree building and finding genetic markers from self-made databases and Summative Tutorial exercise
This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant for the medical sector. WGS technology and applications are high on international political agenda, as the classical methods are being replaced by WGS technology and therefore bioinformatic tools are extremely important for allowing the people working in this sector to be able to analyze the data and obtain results that can be interpreted and used for different purposes. The course will give the learners a basis to understand and be acquainted with WGS applications in surveillance of bacteria including species identification, typing and characterization of antimicrobial resistance and virulence traits as well as plasmid characterization. It will also give the opportunity to learners to learn about online tools and what they can be used for through demonstrations on how to use some of these tools and exercises to be solved by learners with use of freely available WGS analysis tools . By the end of this course you should be able to: 1. Describe the general Principles in typing of Bacteria 2. Give examples of the applications of Whole Genome Sequencing to Surveillance of bacterial pathogens and antimicrobial resistance 3. Apply genomic tools for sub-typing and surveillance 4. Define the concept of Next-Generation Sequencing and describe the sequencing data from NGS 5. Describe how to do de novo assembly from raw reads to contigs 6. Enumerate the methods behind the tools for species identification, MLST typing and resistance gene detection 7. Apply the tools for species identification, MLST typing and resistance gene detection in real cases of other bacterial and pathogen genomes. 8. Describe the methods behind the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing 9. Utilize the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing in real cases of other bacterial and pathogen genomes. 10. Explain the concept and be able to use the integrated bacterial analysis pipeline for batch analysis and typing of genomic data 11. Demonstrate how to construct phylogenetic tree based on SNPs 12. Apply the phylogenetic tool to construct phylogenetic trees and explain the relatedness of bacterial or pathogen strains 13. Describe how to create your own sequence database 14. Utilize the MyDbFinder tool to detect genetic markers of interest from whole genome sequencing
