课程信息
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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. In this course, we teach about the potential of metagenomics for surveillance and give the learners an overview of the steps and considerations in a metagenomics study. After this course, the learners will know: - the difference between the concepts of metagenomics and other microbial genomics - the need to use controls in different steps of a metagenomics study - the advantages of metagenomics for the surveillance of antimicrobial resistance - how sampling design, sample size, sample material and sample handling influence the outcome of a metagenomics study - sample processing for bacterial and viral metagenomics - different sequencing platforms and their possibilities regarding metagenomics - the steps involved in a general metagenomics study, including quality control, mapping to different databases, and read count analysis - the principles behind various tools available for analysis of metagenomics data - how to interpret read classification results - the need for epidemiology in surveillance - the concept of global and integrated surveillance - the challenges for the use of metagenomics in surveillance - the potential of metagenomics for surveillance We look forward to welcoming you !...
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Approx. 13 hours to complete

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Globe

100% 在线课程

立即开始,按照自己的计划学习。
Calendar

可灵活调整截止日期

根据您的日程表重置截止日期。
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Approx. 13 hours to complete

建议:3 weeks of study, 1-3 hours/week...
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English

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教学大纲 - 您将从这门课程中学到什么

Week
1
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完成时间为 3 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. You will also learn about: 1) Sampling and sample handling - the considerations behind a sampling plan, how to perform sampling in practice, and how sample storage can affect metagenomics results; 2) DNA and RNA extraction methods - both for bacterial and viral microorganisms; 3) Sequencing - from library preparation to the basics of different sequencing technologies....
Reading
10 个视频(共 112 分钟), 13 个阅读材料, 2 个测验
Video10 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
Reading13 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
Quiz2 个练习
Module 1 assessment - part 18分钟
Module 1 assessment - part 212分钟
Week
2
Clock
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. ...
Reading
6 个视频(共 64 分钟), 11 个阅读材料, 1 个测验
Video6 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
Reading11 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
Quiz1 个练习
Module 2 assessment24分钟
Week
3
Clock
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 ...
Reading
6 个视频(共 81 分钟), 15 个阅读材料, 6 个测验
Video6 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
Reading15 个阅读材料
Virtual Machine setup分钟
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
Quiz6 个练习
Module 3 assessment10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

讲师

Ana Sofia Ribeiro Duarte

Assistant Professor
National Food Institute

Sünje Johanna Pamp

Associate Professor
Research Group for Genomic Epidemiology, Technical University of Denmark

Liese Van Gompel

PhD Candidate Epidemiology
Utrecht University, Institute for Risk Assessment Sciences (IRAS)

Pimlapas Leekitcharoenphon

PostDoc
Research Group for Genomic Epidemiology, DTU Food

关于 Technical University of Denmark (DTU)

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....

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