PanGBank tutorials

This repository contains runnable tutorials for PanGBank, a web-based platform for exploring, analyzing, and downloading pangenomes built with PPanGGOLiN.

These notebooks walk through real analyses, from AMR gene distribution to genome projection, so you can see PanGBank in action and adapt it to your own data.

PanGBank article use case

The best place to start is the paper use case, a complete end-to-end workflow used in the PanGBank publication:

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN Mainguy J et al. (2026) bioRxiv. doi: 10.64898/2026.08.05.742796

Precomputed data

The paper use case relies on precomputed data that are hosted separately from this repository. The data are automatically downloaded when running the notebook.

The dataset is available from the Zenodo archive.

Note: The precomputed data are not stored in this GitHub repository and do not need to be downloaded manually when using the notebook.

Running locally with Google Colab

Open the notebook directly in Google Colaboratory — no installation required:

Running locally with docker

A self-contained docker image is available to run the tutorials:

docker run -p 8888:8888 ghcr.io/labgem/pangbank-tutorial:latest pangbank-tuto article_use_case

A jupyterlab instance will then be available at http://localhost:8888.

Install the conda environment

git clone https://github.com/labgem/PanGBank-tutorial.git
cd PanGBank-tutorial
conda env create -f environment.yaml
conda activate pangbank-tutorial
pip install pangbank-cli pangbank-api[sdk]==0.5.0 plotly>=6.1.1 kaleido fa2

Then run jupyter-notebook in the tutorial directory:

jupyter-notebook tutorials/article_use_case/notebook.ipynb

Other tutorials

Shorter, standalone notebooks covering focused analyses — several of these were used to build the paper use case above.

Antimicrobial resistance analyses: find Regions of Genome Plasticity (RGPs) and Spots with AMR-related annotations.

name	description	notebook
Acinetobacter_nosocomialis	End-to-end tutorial using a small pangenome.

Genome Projection

name	description	notebook
Projection	Augment a pangenome with AMR annotations, then project a new genome onto the annotated pangenome.

See the tutorials/ directory for the full list of notebooks and examples.