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How to analyze a microbiome

Learn common analysis techniques to make sense of microbial sequencing data.

This course is archived
Estimated 7 weeks
1–3 hours per week
Self-paced
Progress at your own speed
Free
Optional upgrade available
How to analyze a microbiome

About this course

Skip About this course

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.

At a glance

  • Institution: KULeuvenX
  • Subject: Biology & Life Sciences
  • Level: Intermediate
  • 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.
  • Language: English
  • Video Transcript: English

What you'll learn

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  • 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

Syllabus

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Module 0: Introduction
 Study guide, R basics and a help forum for programming questions

Module 1: Introduction to microbiome data
 Sequencing techniques, data types (16S, WGS, metadata), example applications

Module 2: From sequences to counts
 Quality control of reads, taxonomic and functional assignment

Module 3: Comparing microbiomes
 Relative versus absolute abundance, taxonomic and functional richness, evenness and diversity

Module 4: Ordination
 Dimension reduction: arranging samples according to their taxonomic and functional composition in two-dimensional space

Module 5: Taxon/function associations
 Network construction: computing and interpreting associations between taxa and functions

Module 6: Your favourite microbiome
 Databases and journals for microbiome data and guidelines for doing your own analysis

Module 7: Final exam
 Complete the course by passing the quiz or by completing a microbiome analysis

About the instructors

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