Chapter 2 Program

The course takes place on each working day from 9am – 1pm (CEST). Short breaks will be scheduled between sessions.

The hands-on sessions consist of a set of questions and example data. Solve the exercises by taking advantage of the online examples and resources that are pointed out in the study material. There is often more than one way to solve a given task. It is assumed that you have already installed the required software. Do not hesitate to ask support from the course assistants.

2.1 Day 1: from raw sequences to ecological data analysis

Lectures

  • Microbiota analysis: association studies vs. causality; microbiota sequencing methods (16S, shotgun, metagenomics) - by dr. Tom Ederveen (Radboud UMC Nijmegen, The Netherlands)

  • DNA isolation and 16S rRNA gene sequencing; bioinformatics step 1: from raw sequences to OTU table in a biom file – by Tom Ederveen (Radboudumc Nijmegen, The Netherlands)

Demo & Practical

  • Importing data to R for interactive data analysis

  • Task: initialize reproducible report

2.2 Day 2 - Alpha diversity

Demo

  • Microbiome data exploration

Lecture

  • Key concepts in microbiome data science

Practical

  • Alpha diversity: estimation, analysis, and visualization

2.3 Day 3 - Beta diversity

Demo

  • Community similarity

Practical

  • Beta diversity: estimation, analysis, and visualization

2.4 Day 4- Differential abundance

Lecture

  • Differential abundance analysis methods

Practical

  • Differential abundance in practice

Lecture

  • Overview of microbiota data science methods & concepts

2.5 Day 5 : Presentations & closing

Student presentations on microbiome data analytics