Variant-aware CRISPR off-target nomination

Run CRISPRme on your own machine

CRISPRme is open source and actively maintained, and you can run the web interface locally on your own machine with the same functionality as before. The previous hosted application at crisprme.di.univr.it is no longer available, because institutional hosting at the University of Verona ended for this service. All features remain available to you.

You have two easy paths to run CRISPRme on your own machine, both with the same functionality as the previous hosted version:

View on GitHub Installation instructions →

Run CRISPRme on your machine

Pick whichever setup you prefer. Both give you the full command line tool and let you launch the local web interface, which is equivalent to the retired hosted version.

Note: the web-interface must be launched from within the CRISPRme directory tree, just like the command line version, so that all required resources and paths are correctly resolved. If you are unsure about the expected project structure, please refer to the directory structure documentation.

Before launching the web interface, install CRISPRme and download the legacy reference datasets. This setup only needs to be completed once.

Download the Legacy Reference Database

The setup command automatically downloads and configures:

# Choose a working directory
CRISPRME_DIR="$HOME/my_crisprme_run"

# Download and configure all reference data
crisprme.py setup --path "$CRISPRME_DIR"

Optional: If you want to test the installation before downloading the complete dataset (~410 GB), perform a chromosome-specific setup first: 

crisprme.py setup --chrom chr22 --path "$CRISPRME_DIR"

The setup process is resumable. If a download is interrupted, simply rerun the same command and CRISPRme will continue from the last completed step.

Launching the local web-interface

Option 1: Docker

docker pull pinellolab/crisprme
docker run -v ${PWD}:/DATA -w /DATA -p 8080:8080 pinellolab/crisprme crisprme.py web-interface

Option 2: Conda / Mamba

mamba create -n crisprme python=3.9 crisprme -y
mamba activate crisprme
crisprme.py --version
crisprme.py web-interface

After the server starts, open your browser and navigate to: 

http://127.0.0.1:8080

Supported browsers include Chrome, Firefox, and Safari.

Important: Start the web interface from a valid CRISPRme working directory containing the expected folders (Genomes/, VCFs/, PAMs/, Annotations/, etc.), otherwise datasets and configuration files will not be detected.

Advanced Resources & Documentation

The quick-start guide above is sufficient to get the local web interface running. For detailed usage instructions, advanced configuration options, and complete workflow documentation, consult the guides below.

Web Interface User Guide

Learn how to configure analyses, monitor jobs, explore results, generate personal risk cards, and use all visualization and reporting features available through the graphical interface.

Open Detailed User Guide

CLI Setup & Usage Guide

Complete documentation for installation, dataset management, command-line workflows, custom VCF integration, PAM definition, automation, and large-scale analyses.

Open CLI Guide

Documentation

Citation

Cancellieri S, Zeng J, Lin LY, Tognon M, Nguyen MA, Lin J, Bombieri N, Maitland SA, Ciuculescu MF, Katta V, Tsai SQ, Armant M, Wolfe SA, Giugno R, Bauer DE, Pinello L. Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nat Genet. 2023 Jan;55(1):34-43. doi: 10.1038/s41588-022-01257-y.

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