Informações sobre o curso
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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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Sugerido: 3 weeks of study, 1-3 hours/week

Aprox. 13 horas restantes
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English

Legendas: English
Globe

cursos 100% online

Comece imediatamente e aprenda em seu próprio cronograma.
Calendar

Prazos flexíveis

Redefinir os prazos de acordo com sua programação.
Clock

Sugerido: 3 weeks of study, 1-3 hours/week

Aprox. 13 horas restantes
Comment Dots

English

Legendas: English

Programa - O que você aprenderá com este curso

1

Seção
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3 horas para concluir

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 vídeos (Total de 112 min), 13 leituras, 2 testes
Video10 videos
Welcome14min
Introduction to metagenomics10min
Considerations and controls for metagenomic/microbiome projects10min
Introduction to antimicrobial resistance11min
Sampling for surveillance18min
Sampling at farms and slaughterhouses14min
Sample storage2min
Isolation of DNA from complex samples10min
Sample processing for viral metagenomics7min
Sequencing platforms12min
Reading13 leituras
Glossary20min
Get started !5min
Introduction to metagenomics2min
Considerations and controls for metagenomic/microbiome projects2min
Introduction to antimicrobial resistance2min
Sampling for surveillance5min
Sampling at farms and slaughterhouses2min
Sample storage2min
Isolation of DNA from complex samples2min
Notes on library preparation5min
Sequencing platforms10min
Assessment case-study - part 15min
Assessment case study - part 22min
Quiz2 exercícios práticos
Module 1 assessment - part 18min
Module 1 assessment - part 212min

2

Seção
Clock
3 horas para concluir

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 vídeos (Total de 64 min), 11 leituras, 1 teste
Video6 videos
Overview of available metagenomic analysis tools7min
MGmapper13min
ResFinder database5min
Demo of metagenomic classification using KRAKEN16min
Real example of metagenomic analysis - lessons learned14min
Reading11 leituras
General introduction to bioinformatics analysis of metagenomics data5min
Overview of available metagenomic analysis tools10min
MGmapper10min
MGmapper - Best mode vs Full mode10min
ResFinder database3min
Assessment case-study - part 310min
Samples sheet10min
Report A - FastQC results10min
Report B - MGmapper results10min
Report C - KRAKEN results10min
Report D10min
Quiz1 exercícios práticos
Module 2 assessment24min

3

Seção
Clock
8 horas para concluir

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 vídeos (Total de 81 min), 15 leituras, 6 testes
Video6 videos
Metagenomic assembly and binning: reconstructing genomes from reads15min
Application of metagenomics in surveillance - methods (part 1)10min
Application of metagenomics in surveillance - methods (part 2)16min
Application of metagenomics in surveillance - opportunities and challenges21min
Farewell3min
Reading15 leituras
Virtual Machine setupmin
Analysis and visualization of read count data10min
Metagenomic assembly and binning: reconstructing genomes from reads10min
Application of metagenomics in surveillance - methods10min
Potential of metagenomics for surveillance10min
Challenges of metagenomics for surveillance10min
Assessment case-study - part 45min
Report D10min
Epidemiology sheet and Report E10min
Introduction5min
Final quiz - section I - Sampling10min
Final quiz - section II - Quality control30min
Final quiz - section III - Bioinformatics analysis of metagenomics30min
Final quiz - section IV - Interpretation of metagenomics results10min
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context10min
Quiz6 exercícios práticos
Module 3 assessment10min
Final quiz - section I - Sampling18min
Final quiz - section II - Quality control30min
Final quiz - section III - Bioinformatics analysis of metagenomics30min
Final quiz - section IV - Interpretation of metagenomics results30min
Final quiz - section V - Analysis of metagenomics results in a surveillance context30min

Instrutores

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

Sobre 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....

Perguntas Frequentes – FAQ

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  • When you purchase a Certificate you get access to all course materials, including graded assignments. Upon completing the course, your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.

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