This repository contains materials accompanying the metagenomics hands-on workshop of the Rigi Workshop 2025: Microbiome Meets Metabolism. To jump directly to the analysis notebooks, click on the badges for the corresponding tutorials below.
The notebook included in this repository describes simplified analyses of microbiome datasets using the with the MOSHPIT toolkit, built on the QIIME 2 framework. To learn more about the QIIME 2 project and applications in microbiome research, visit https://qiime2.org/.
In this notebook, we use feature tables generated for MAGs obtained from analysis of coca beans fermentation (see the original study here). To launch, click on the badge above.
This analysis notebook builds on top of the MOSHPIT tutorial.
The setup script to deploy MOSHPIT on Google Colab has been adapted from the Advanced Block Course: Computational Biology; all source code is licensed under the Apache License 2.0.
This workshop uses Google Colab for ease of use in a workshop setting. However, the computational environment and resource restrictions are not well suited for analysis of metagenome data in a real experimental setting, including analysis of raw DNA sequencing data. To use MOSHPIT to analyze real data, refer to the tutorial above for installation instructions.
Moreover, the setup script used here is specific to our Colab deployment. DO NOT ATTEMPT TO RUN THIS SETUP SCRIPT OR NOTEBOOK LOCALLY!
All source code is licensed under the Apache License 2.0.
