Metagenomics I#
General information#
With these exercises, we aim to explore the concepts and approaches in metagenomics data analysis that we discussed in the lectures. We will work both on a small dataset from a defined microbial community to explore and understand the concepts and on large real datasets to identify the issues and shortcomings of different approaches. We will write, understand, and modify R-code according to analytical needs.
For the first exercise session, we will explore how to describe a microbial community. Modern analysis of microbiome samples is based on DNA sequencing, and here we will focus on 16S amplicon sequencing data. In these exercises we will:
Explore the concepts of Amplicon Sequence Variants (ASVs) and Operational Taxonomic Units (OTUs). In the context of OTUs, we will also get familiar with a general algorithm to cluster sequences at different identity thresholds.
Use a taxonomic profiling table as a means to explore data structure and work with different taxonomic ranks.
Calculate and compare alpha-diversity metrics, i.e. metrics describing a single microbial community.
Resources#
Exercises within the Metagenomics I section require the use of the R-Studio on cousteau: http://cousteau-rstudio.ethz.ch/
If you do not feel confident in R, we highly recommend to do the R refresher before proceeding with the exercises.