The field of metagenomics and whole community sequencing is a promising area to unravel the content of microbial communities and their relationship to disease and antimicrobial resistance in the human population. Bioinformatic tools are extremely important for making sense out of metagenomics data, by estimating the presence of pathogens and antimicrobial resistance determinants in complex samples. Combined with relevant explanatory data, metagenomics is a powerful tool for surveillance.
Metagenomics applied to surveillance of pathogens and antimicrobial resistance
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完成时间大约为15 小时
英语（English）
字幕：英语（English）
讲师
学生职业成果
67%
完成这些课程后已开始新的职业生涯
60%
通过此课程获得实实在在的工作福利
25%
加薪或升职
可分享的证书
完成后获得证书
100% 在线
立即开始，按照自己的计划学习。
可灵活调整截止日期
根据您的日程表重置截止日期。
完成时间大约为15 小时
英语（English）
字幕：英语（English）
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丹麦技术大学
DTU focuses on research in technical and natural sciences that contributes to the development of society. As an industrially orientated university, our goal is to supply high-level international research based on combining theory with constructing models and empirical methods.
教学大纲 - 您将从这门课程中学到什么
完成时间为 4 小时
From sampling to sequencing
In this module, you will be introduced to metagenomics, some of the considerations and controls that need to be in place in a metagenomics study, and to the topic of antimicrobial resistance.
完成时间为 4 小时
10 个视频 （总计 112 分钟）, 13 个阅读材料, 2 个测验
10 个视频
Welcome14分钟
Introduction to metagenomics10分钟
Considerations and controls for metagenomic/microbiome projects10分钟
Introduction to antimicrobial resistance11分钟
Sampling for surveillance18分钟
Sampling at farms and slaughterhouses14分钟
Sample storage2分钟
Isolation of DNA from complex samples10分钟
Sample processing for viral metagenomics7分钟
Sequencing platforms12分钟
13 个阅读材料
Glossary20分钟
Get started !5分钟
Introduction to metagenomics2分钟
Considerations and controls for metagenomic/microbiome projects2分钟
Introduction to antimicrobial resistance2分钟
Sampling for surveillance5分钟
Sampling at farms and slaughterhouses2分钟
Sample storage2分钟
Isolation of DNA from complex samples2分钟
Notes on library preparation5分钟
Sequencing platforms10分钟
Assessment case-study - part 15分钟
Assessment case study - part 22分钟
2 个练习
Module 1 assessment - part 130分钟
Module 1 assessment - part 230分钟
完成时间为 3 小时
FROM READS TO RESULTS
In this module, you will be introduced to the basics of bioinformatics analysis of metagenomics data, including the different types of analysis possible and the different algorithms available. You will then learn about quality control, MGmapper and KRAKEN (two freely available bioinformatics pipelines), and ResFinder (a database of antimicrobial resistance genes). An example from a real study will demonstrate some of the challenges of a bioinformatics analysis.
完成时间为 3 小时
6 个视频 （总计 64 分钟）, 11 个阅读材料, 1 个测验
6 个视频
Overview of available metagenomic analysis tools7分钟
MGmapper13分钟
ResFinder database5分钟
Demo of metagenomic classification using KRAKEN16分钟
Real example of metagenomic analysis - lessons learned14分钟
11 个阅读材料
General introduction to bioinformatics analysis of metagenomics data5分钟
Overview of available metagenomic analysis tools10分钟
MGmapper10分钟
MGmapper - Best mode vs Full mode10分钟
ResFinder database3分钟
Assessment case-study - part 310分钟
Samples sheet10分钟
Report A - FastQC results10分钟
Report B - MGmapper results10分钟
Report C - KRAKEN results10分钟
Report D10分钟
1 个练习
Module 2 assessment30分钟
完成时间为 8 小时
Interpretation of results and potential of metagenomics for surveillance
In this module you will learn about two different approaches to analyse and interpret sequence reads - classification and assembly. You will see examples of methods to vizualize read counts and to analyze metagenomics together with explanatory data. Last, you will learn the potential of metagenomics for the development of a future global and integrated surveillance, and the challenges you may encounter during that process
完成时间为 8 小时
6 个视频 （总计 81 分钟）, 16 个阅读材料, 6 个测验
6 个视频
Metagenomic assembly and binning: reconstructing genomes from reads15分钟
Application of metagenomics in surveillance - methods (part 1)10分钟
Application of metagenomics in surveillance - methods (part 2)16分钟
Application of metagenomics in surveillance - opportunities and challenges21分钟
Farewell3分钟
16 个阅读材料
Virtual Machine setup1小时
Analysis and visualization of read count data10分钟
Metagenomic assembly and binning: reconstructing genomes from reads10分钟
Application of metagenomics in surveillance - methods10分钟
Potential of metagenomics for surveillance10分钟
Challenges of metagenomics for surveillance10分钟
Assessment case-study - part 45分钟
Report D10分钟
Epidemiology sheet and Report E10分钟
Introduction5分钟
Final quiz - section I - Sampling10分钟
Final quiz - section II - Quality control30分钟
Final quiz - section III - Bioinformatics analysis of metagenomics30分钟
Final quiz - section IV - Interpretation of metagenomics results10分钟
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context10分钟
Extra material for final assessment10分钟
6 个练习
Module 3 assessment30分钟
Final quiz - section I - Sampling18分钟
Final quiz - section II - Quality control30分钟
Final quiz - section III - Bioinformatics analysis of metagenomics30分钟
Final quiz - section IV - Interpretation of metagenomics results30分钟
Final quiz - section V - Analysis of metagenomics results in a surveillance context30分钟
审阅
来自METAGENOMICS APPLIED TO SURVEILLANCE OF PATHOGENS AND ANTIMICROBIAL RESISTANCE的热门评论
由 MQ 提供Apr 16, 2020
This course proved helpful in anticipating the very basic idea of metagenomics analysis along with the useful explanation of data interpretation to dig out appropriate results.
由 IA 提供Oct 28, 2020
I really enjoyed the course. Covered all aspects of a metagenomics project in surveillance of pathogens and AMR, from study design to data analysis and result interpretation.
由 MD 提供May 30, 2019
I learned a lot, they covered complex analysis topics in a clear, understandable way. I would recommend this course to anyone interested in microbial metagenomic analysis.
由 DD 提供Aug 1, 2020
The course was well structured however I had little difficulty in doing last assignments I think some session on problem solving should be done before giving assignments.
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