Microbiome analysis

This track introduces microbiome data analysis using Galaxy, covering both foundational and advanced workflows.

It begins with metabarcoding / amplicon-based analysis using DADA2, a widely adopted standard approach for processing and visualizing microbiome data, which can be directly applied to real-world datasets.

The read-based metagenomics section introduces taxonomic classification using Kraken2 and MetaPhlAn, along with downstream diversity analysis. It covers how sequencing reads are assigned to microbial taxa using both k-mer–based and marker gene–based approaches, how classification results can be interpreted, and how community composition can be explored using diversity metrics and visualizations. Together, these steps provide a foundation for understanding microbial community structure directly from sequencing reads without the need for assembly.

The Metagenome-Assembled Genomes (MAGs) section provides a comprehensive overview of MAG generation, developed in collaboration with the FAIRyMAGs project. It includes all key steps: quality control, removal of host and contaminant reads, assembly, binning (demonstrated with four different tools), bin refinement, and functional annotation.

A complete end-to-end workflow is provided as a foundation for analyzing your own samples. The track then progresses to more advanced topics, including metatranscriptomics and pathogen detection.

You can start with the tutorials at your own pace. However, if you plan to work through the MAG workflow, we recommend allocating several days, as it is a complex and computationally intensive topic.

If you need support, contact us via the Slack channel gta_microbiome.

🚨 The workflows used for this track were tested thoroughly on the EU server. If you encounter any issues with execution on other servers, we recommend retrying the tutorial on usegalaxy.eu!

Organiser(s)	Paul Zierep Bérénice Batut
Instructor(s)	Anna Syme Bérénice Batut Engy Nasr Gareth Price Igor Makunin Jennifer Hillman-Jackson Matthias Bernt Paul Zierep Polina Polunina Rand Zoabi Saim Momin Pratik Jagtap Santino Faack Giuseppe Defazio Mina Hojat Ansari