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
丹麦技术大学課程信息
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完成時間大約為15 小時
英語（English）
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講師
學生職業成果
67%
完成這些課程後已開始新的職業生涯
60%
通過此課程獲得實實在在的工作福利
25%
加薪或升職
可分享的證書
完成後獲得證書
100% 在線
立即開始，按照自己的計劃學習。
可靈活調整截止日期
根據您的日程表重置截止日期。
完成時間大約為15 小時
英語（English）
字幕：英語（English）
提供方
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.
教學大綱 - 您將從這門課程中學到什麼
完成時間為 4 小時
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.
完成時間為 4 小時
10 個視頻 （總計 112 分鐘）, 13 個閱讀材料, 2 個測驗
10 個視頻
Welcome14分鐘
Introduction to metagenomics10分鐘
Considerations and controls for metagenomic/microbiome projects10分鐘
Introduction to antimicrobial resistance11分鐘
Sampling for surveillance18分鐘
Sampling at farms and slaughterhouses14分鐘
Sample storage2分鐘
Isolation of DNA from complex samples10分鐘
Sample processing for viral metagenomics7分鐘
Sequencing platforms12分鐘
13 個閱讀材料
Glossary20分鐘
Get started !5分鐘
Introduction to metagenomics2分鐘
Considerations and controls for metagenomic/microbiome projects2分鐘
Introduction to antimicrobial resistance2分鐘
Sampling for surveillance5分鐘
Sampling at farms and slaughterhouses2分鐘
Sample storage2分鐘
Isolation of DNA from complex samples2分鐘
Notes on library preparation5分鐘
Sequencing platforms10分鐘
Assessment case-study - part 15分鐘
Assessment case study - part 22分鐘
2 個練習
Module 1 assessment - part 130分鐘
Module 1 assessment - part 230分鐘
完成時間為 3 小時
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.
完成時間為 3 小時
6 個視頻 （總計 64 分鐘）, 11 個閱讀材料, 1 個測驗
6 個視頻
Overview of available metagenomic analysis tools7分鐘
MGmapper13分鐘
ResFinder database5分鐘
Demo of metagenomic classification using KRAKEN16分鐘
Real example of metagenomic analysis - lessons learned14分鐘
11 個閱讀材料
General introduction to bioinformatics analysis of metagenomics data5分鐘
Overview of available metagenomic analysis tools10分鐘
MGmapper10分鐘
MGmapper - Best mode vs Full mode10分鐘
ResFinder database3分鐘
Assessment case-study - part 310分鐘
Samples sheet10分鐘
Report A - FastQC results10分鐘
Report B - MGmapper results10分鐘
Report C - KRAKEN results10分鐘
Report D10分鐘
1 個練習
Module 2 assessment30分鐘
完成時間為 8 小時
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
完成時間為 8 小時
6 個視頻 （總計 81 分鐘）, 16 個閱讀材料, 6 個測驗
6 個視頻
Metagenomic assembly and binning: reconstructing genomes from reads15分鐘
Application of metagenomics in surveillance - methods (part 1)10分鐘
Application of metagenomics in surveillance - methods (part 2)16分鐘
Application of metagenomics in surveillance - opportunities and challenges21分鐘
Farewell3分鐘
16 個閱讀材料
Virtual Machine setup1小時
Analysis and visualization of read count data10分鐘
Metagenomic assembly and binning: reconstructing genomes from reads10分鐘
Application of metagenomics in surveillance - methods10分鐘
Potential of metagenomics for surveillance10分鐘
Challenges of metagenomics for surveillance10分鐘
Assessment case-study - part 45分鐘
Report D10分鐘
Epidemiology sheet and Report E10分鐘
Introduction5分鐘
Final quiz - section I - Sampling10分鐘
Final quiz - section II - Quality control30分鐘
Final quiz - section III - Bioinformatics analysis of metagenomics30分鐘
Final quiz - section IV - Interpretation of metagenomics results10分鐘
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context10分鐘
Extra material for final assessment10分鐘
6 個練習
Module 3 assessment30分鐘
Final quiz - section I - Sampling18分鐘
Final quiz - section II - Quality control30分鐘
Final quiz - section III - Bioinformatics analysis of metagenomics30分鐘
Final quiz - section IV - Interpretation of metagenomics results30分鐘
Final quiz - section V - Analysis of metagenomics results in a surveillance context30分鐘
審閱
來自METAGENOMICS APPLIED TO SURVEILLANCE OF PATHOGENS AND ANTIMICROBIAL RESISTANCE的熱門評論
由 MQ 提供2020年4月16日
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 MD 提供2019年5月30日
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2020年8月1日
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.
由 B 提供2020年6月22日
overall good learning as well they have given detailed and understandable knowledge which can help in future to identify as many as resistance gene to cure diseases
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