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.

Option 1: Docker

docker pull pinellolab/crisprme
docker run -v ${PWD}:/DATA -w /DATA -i 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

Then open the URL printed in your terminal in a browser (Chrome, Firefox, or Safari).

Quick test

Verify the installation with a small-scale test on chromosome 22 using the 1000 Genomes dataset:

crisprme.py complete-test --chrom chr22 --vcf_dataset 1000G

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.

Contacts