trytoolchest/getting-started-python-jupyter

This notebook takes one 16S sample from an Illumina MiSeq run, runs it through Kraken 2 on Toolchest, and plots a rough sketch of the microbial composition of the sample.

Getting started with Toolchest in Python

Intro

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

Setup

Python dependencies

Quickest: from this directory, runpip install -r ./requirements.txt

Manual: install matplotlib, toolchest-client, and pandas

Toolchest key

Sign up for a free key, and replace the call to toolchest.set_key("YOUR_KEY_HERE") with your key.

Installing Jupyter

If you don't already have Toolchest installed locally, follow the Jupyter install guide.

Running

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.