This repo has a Jupyter notebook with a basic microbiome analysis – from raw FASTQs to plots.
If you'd rather jump straight to a working version of this Jupyter notebook, head over to https://www.trytoolchest.com/getting-started-with-toolchest-python
Quickest: from this directory, runpip install -r ./requirements.txt
Manual: install matplotlib, toolchest-client, and pandas
Sign up for a free key, and replace the call to toolchest.set_key("YOUR_KEY_HERE") with your key.
If you don't already have Toolchest installed locally, follow the Jupyter install guide.
Run jupyter notebook microbiome_analysis.ipynb from inside the project to start a Jupyter notebook.
That should be it! You can advance through the notebook with the "Run" button, or however you like to run Jupyter notebooks.