Metagenomics applied to surveillance of pathogens and antimicrobial resistance
- 4.7
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Approx. 15 hours to complete
Course Summary
This course introduces the field of metagenomics and the application of next-generation sequencing technologies in studying microbial communities. It covers the computational tools and techniques used to analyze and interpret metagenomic data.Key Learning Points
- Learn about the use of next-generation sequencing technologies in studying microbial communities
- Understand the computational tools used to analyze metagenomic data
- Gain knowledge on the interpretation of metagenomic data
Related Topics for further study
- next-generation sequencing
- microbial communities
- metagenomic data analysis
- computational tools
- microbiome
Learning Outcomes
- Understand the basics of metagenomics
- Learn about the different tools used to analyze metagenomic data
- Be able to interpret metagenomic data
Prerequisites or good to have knowledge before taking this course
- Basic understanding of biology and genomics
- Familiarity with programming languages such as Python
Course Difficulty Level
IntermediateCourse Format
- Online self-paced course
- Video lectures
- Quizzes and assignments
Similar Courses
- Introduction to Genomic Technologies
- Bioinformatics Specialization
Notable People in This Field
- Dr. Eran Segal
- Dr. Rob Knight
Related Books
Description
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.
Outline
- From sampling to sequencing
- Welcome
- Introduction to metagenomics
- Considerations and controls for metagenomic/microbiome projects
- Introduction to antimicrobial resistance
- Sampling for surveillance
- Sampling at farms and slaughterhouses
- Sample storage
- Isolation of DNA from complex samples
- Sample processing for viral metagenomics
- Sequencing platforms
- Glossary
- Get started !
- Introduction to metagenomics
- Considerations and controls for metagenomic/microbiome projects
- Introduction to antimicrobial resistance
- Sampling for surveillance
- Sampling at farms and slaughterhouses
- Sample storage
- Isolation of DNA from complex samples
- Notes on library preparation
- Sequencing platforms
- Assessment case-study - part 1
- Assessment case study - part 2
- Module 1 assessment - part 1
- Module 1 assessment - part 2
- FROM READS TO RESULTS
- General introduction to bioinformatics analysis of metagenomics data
- Overview of available metagenomic analysis tools
- MGmapper
- ResFinder database
- Demo of metagenomic classification using KRAKEN
- Real example of metagenomic analysis - lessons learned
- General introduction to bioinformatics analysis of metagenomics data
- Overview of available metagenomic analysis tools
- MGmapper
- MGmapper - Best mode vs Full mode
- ResFinder database
- Assessment case-study - part 3
- Samples sheet
- Report A - FastQC results
- Report B - MGmapper results
- Report C - KRAKEN results
- Report D
- Module 2 assessment
- Interpretation of results and potential of metagenomics for surveillance
- Analysis and visualization of read count data
- Metagenomic assembly and binning: reconstructing genomes from reads
- Application of metagenomics in surveillance - methods (part 1)
- Application of metagenomics in surveillance - methods (part 2)
- Application of metagenomics in surveillance - opportunities and challenges
- Farewell
- Virtual Machine setup
- Analysis and visualization of read count data
- Metagenomic assembly and binning: reconstructing genomes from reads
- Application of metagenomics in surveillance - methods
- Potential of metagenomics for surveillance
- Challenges of metagenomics for surveillance
- Assessment case-study - part 4
- Report D
- Epidemiology sheet and Report E
- Introduction
- Final quiz - section I - Sampling
- Final quiz - section II - Quality control
- Final quiz - section III - Bioinformatics analysis of metagenomics
- Final quiz - section IV - Interpretation of metagenomics results
- Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context
- Extra material for final assessment
- Module 3 assessment
- Final quiz - section I - Sampling
- Final quiz - section II - Quality control
- Final quiz - section III - Bioinformatics analysis of metagenomics
- Final quiz - section IV - Interpretation of metagenomics results
- Final quiz - section V - Analysis of metagenomics results in a surveillance context
Summary of User Reviews
Key Aspect Users Liked About This Course
The engaging lecturesPros from User Reviews
- Hands-on assignments
- Real-world applications
- Flexible pace
Cons from User Reviews
- Challenging for beginners
- Some technical issues
- Limited interaction with instructors
Ana Sofia Ribeiro Duarte
4.7 Raiting
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Metagenomics applied to surveillance of pathogens and antimicrobial resistance
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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....
