Junction dataset

This repository contains a simple pipeline to prepare and format the dataset of genomic junctions from the E. coli ST131 collection described in our paper.

Setup

To run the pipeline you will need to have Snakemake (tested on v9.11) and Conda installed. Moreover you will need to have the PanGraph (v1.2.1) binary available in your PATH.

Usage

Run the pipeline simply with:

snakemake --use-conda --cores <num_cores> all

Viewing junctions

You can explore junctions visually with marimo by running:

marimo run explore/view_junctions.py