README.md

PanGBank tutorials

Quick start

Running tutorials on Google Colab

All tutorials are available on Google Colab, see the Tutorials section.

Running locally with docker

A self-contained docker is available to run the tutorials

docker run -p 8888:8888 ghcr.io/labgem/pangbank-tutorial:latest pangbank-tuto <tutorial_name>

Then a jupyterlab instance is available at http://localhost:8888.

Running locally with conda

Warning

Cloning the repository requires git-lfs.

• deb: apt install git-lfs
• rmp: dnf install git-lfs

Install the conda environment

git clone https://github.com/labgem/PanGBank-tutorial.git
cd PanGBank-tutorial
conda create env -f environment.yaml
conda activate pangbank-tutorial
pip install pangbank-cli

Then run jupyter-notebook in the tutorial directory

cd tutorials/<tutorial_name> && jupyter-notebook notebook.ipynb

Warning

The notebook code expects the current working directory to be the one containing the notebook notebook.ipynb. Be sure to launch Jupyter in the correct directory.

Tutorials

Antimicrobial resistance analysis

Find Regions of Genome Plasticity (RGPs) and Spots with AMR-related annotations.

name	description	notebook
Acinetobacter_baumannii	Downstream analysis based on pre-computed PPanGGOLiN outputs.
Acinetobacter_nosocomialis	End-to-end tutorials using a small pangenome

Genome Projection

name	description	notebook
Projection	Augment a pangenome with AMR annotations and then project a new genome on the annotated pangenome