PaintSHOP is a technology that enables the interactive design of oligonucleotide FISH experiments at genome and transcriptome-scale and is comprised of two components:

1. A scalable machine learning pipeline for probe specifity prediction

2. An interactive Shiny web application for probe design

This repository contains the Snakemake workflow for the machine learning pipeline and the full software stack needed to design probes for additional genomes not already hosted on the web application.

1. Make sure you have conda installed.

2. Clone this repo, then create and activate the provided environment:

$ git clone https://github.com/beliveau-lab/PaintSHOP_pipeline.git \
    && cd PaintSHOP_pipeline/ \
    && conda env create -f environment.yml \
    && conda activate paintshop_snakemake

A complete example is included to test the pipeline installation. To run the pipeline on the included sample files:

$ cd example_run/ && ./run_pipeline.sh

When this example is run, pipeline output will be generated here. Expected outputs are provided here for comparison.

To run the pipeline on your own data, update the file paths in config.yml with the paths to your genome assembly files. For more information on input and output files, see the documentation.

This pipeline is implemented using Snakemake, and distributed according to best practices. If you are new to Snakemake, the tutorial is a great place to get started to learn more.

Additional information is available in the docs:

• Input file specification
• Output file specification
• Description of pipeline steps

If you have questions or issues, please open an issue on GitHub.

For usage of the pipeline and/or web application, please cite according to the enclosed citation.bib.

We provide this open source software without any warranty under the MIT license.