CRISPRCasFinder is an updated, improved, and integrated version of CRISPRFinder and CasFinder.

If you use this software, please cite:

• Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7. DOI: https://doi.org/10.1093/nar/gkm360 PMID:17537822

• Abby SS, Néron B, Ménager H, Touchon M, Rocha EP. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One. 2014 Oct 17;9(10):e110726. DOI: https://doi.org/10.1371/journal.pone.0110726 PMID:25330359

• Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251. DOI: https://doi.org/10.1093/nar/gky425 PMID:29790974

• Néron B, Denise R, Coluzzi C, Touchon M, Rocha EPC, Abby SS (2022). MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. bioRxiv DOI: 10.1101/2022.09.02.506364 Link

Further information are available at: https://crisprcas.i2bc.paris-saclay.fr.

Note that you will first need to install conda/bioconda to run the following commands:

conda env create -f ccf.environment.yml -n crisprcasfinder
conda activate crisprcasfinder
mamba init
mamba activate
mamba install -c bioconda macsyfinder=2.1.2
macsydata install -u CASFinder==3.1.0

./installer_MAC.sh

bash installer_UBUNTU.sh
source ~/.profile

Please first install conda if it is not already installed:

sudo yum -y update
sudo yum -y upgrade
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
export PATH=/path/to/miniconda3/bin/:$PATH
source ~/.bashrc
conda init
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Now you can install CRISPRCasFinder as follows:

bash installer_CENTOS.sh
exit #this command could be needed if your command prompt changes
source ~/.bashrc

sudo yum -y update
sudo yum -y upgrade
bash installer_FEDORA.sh
source ~/.bashrc

You can run the command 'perl CRISPRCasFinder.pl -v' to see if everything is OK. You may need to reinstall some Perl's modules (with command: sudo cpanm ...), for example: "sudo cpanm Date::Calc". The notification "Possible precedence issue with control flow operator ..." will not affect results of analysis. For further information, please see the documentation.

perl CRISPRCasFinder.pl -in install_test/sequence.fasta -cas -keep

For further details, please see the documentation.

A more complete User Manual is available at the following file : CRISPRCasFinder_Viewer_manual.pdf

GPL v3

If you want to try CRISPRCasFinder without installing dependencies, The standalone version is also available as a singularity container (hosted on the Download page of the CRISPR-Cas++ portal):

After downloading the CrisprCasFinder.simg image from the CRISPR-Cas++ Download page, you can for example run the following command (sequence.fasta file must be replaced by your file):

singularity exec -B $PWD CrisprCasFinder.simg perl /usr/local/CRISPRCasFinder/CRISPRCasFinder.pl -so /usr/local/CRISPRCasFinder/sel392v2.so -cf /usr/local/CRISPRCasFinder/CasFinder-2.0.3 -drpt /usr/local/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /usr/local/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RES21092020_2 -in sequence.fasta

Please visit the following link for more information about singularity containers: https://www.sylabs.io/docs/