COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites (CRISPR-COPIES) is a user-friendly web application and a command line tool for rapid discovery of neutral integration sites. Designed to work for any organism with a genome in NCBI and for any CRISPR system, CRISPR-COPIES can identify neutral sites in a genome-wide manner. The identified sites can be used for characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.
This repository accompanies the work "CRISPR-COPIES: An in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration".
You can use CRISPR-COPIES through our web interface. Visit us at CRISPR-COPIES.
Note: We have restricted the web interface to prokaryotic and small eukaryotic genomes. We advise you to use our command line option for genomes greater than 120 Mb in size as significant time and computation resources are required.
bash setup.sh
source venv38/bin/activate
pip install -r requirements38.txt
CRISPR-COPIES can also be accessed using the command line. For information on parameters, run
python code/main.py -h
A sample example to run the script -
python code/main.py -g ../data/s288c/GCF_000146045.2_R64_genomic.fna -t ../data/s288c/GCF_000146045.2_R64_feature_table.txt -p NGG -o 3prime -l 20 -sl 10 --edit_dist 6 --intspace 350 -out ../data/s288c/output.csv --distal_end_len 10000 -hr_l 50 --protein_file ../data/s288c/GCF_000146045.2_R64_protein.faa
Note: -look or --lookup arguement is implemented to perform a fuzzy text search for the web application. One needs to specify the genome file, protein fasta file, and the corresponding feature table to run the command line tool. #Add files for essential gene search
Detailed information and sample values of parameters for different organisms is provided here.