Syllabus
Instructors
Course Staff
- Karoline Faust: Assistant Professor at KU Leuven
- Lisa Röttjers: PhD candidate at KU Leuven
View the about page of this course
Description
Microorganisms play a major role in the biosphere and within our bodies, but only a tiny fraction has been cultured so far. Microbiome data, that is the genetic information of microorganisms, is therefore an important window into the hidden microbial world.
Microbiome data analysis elucidates the composition of microbial communities and how it changes in response to the environment. When analyzing sequencing data, we learn whether microbial diversity differs across conditions and identify links between microbes. In brief, microbiome data analysis gives us a first idea of how a microbial ecosystem works.
This course will illustrate with the help of real-world example data how to carry out typical analysis tasks, such as comparing microbial composition and diversity, clustering samples and computing associations. If you plan to work with microbiome data, this course will get you up to speed.
The instructors are experienced bioinformaticians who are internationally known for their analysis of large-scale microbiome data sets.
Prerequisites
- Basic knowledge of biology is required throughout the course.
- Basic knowledge of statistics and programming is required to complete specific sections of this course.
Duration and Work Load
The course is a self-paced course and will be available until 15/12/2020.
The course contains 7 modules and it would be realistic to spend 1 to 3 hours on each module.
Learning Outcomes and Objectives
- How and why microbiome data are collected
- How to extract species and function counts from sequencing data
- The definitions of richness, evenness and diversity
- How to compare diversity and microbial composition across conditions
- How to compute and interpret taxon and function associations
Modules:
- Module 1: Introduction to microbiome data
- Module 2: DNA to counts
- Module 3: Compare microbiomes
- Module 4: Ordination
- Module 5: Associations
- Module 6: Your favourite microbiome
Grading
This course has 2 different options for the examination. You can choose to do one of them, or both, in which case only the best grade will be assessed. A score above 65 is required to pass the course.
- Assignment: Carry out an analysis on microbiome data of your choice. This analysis will be peer-reviewed for grading.
- Quiz: A series of questions about all the modules. None of the questions require programming.