- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Tools for comparative metagenomics
In this session Georg Zeller, group leader at EMBL, covers some comparative analyses that can be carried on metagenomics data. Georg uses disease vs healthy human gut data as example data within this talk, but the tools and methods discussed are applicable to any metagenomic data. This talk covers various comparisons and statistical tests that can be useful, including statistical modelling and machine leaning approaches, and highlights some potential pitfalls and caveats for each approach.
Practical
In this practical, you will explore statistical testing methods for metagenomic data, learn how to visualize the experimental results, and then train a machine learning models using the SIAMCAT package.
- Practical guide: Comparative metagenomics EMBL GitHub
- Alternative location: ZellerLab GitHub
- Use this if the git.embl.de domain does not work
You can find the SIAMCAT toolbox, BioConductor package and preprint (including large-scale application) below: