CRISPR-PLANTv2

Repository for CRISPR-PLANT version 2 pipeline accompanying the manuscript "CRISPR-PLANT v2: An online resource for highly specific guide RNA spacers based on improved off-target analysis" published in The Plant Biotechnology Journal.

Reference

https://doi.org/10.1111/pbi.13025

Dependencies

The pipeline is dependent on the following packages

1. python2
2. usearch https://www.drive5.com/usearch/
3. vsearch https://github.com/torognes/vsearch
4. emboss http://emboss.sourceforge.net/

Content

1. directory "python-scripts": Contains all files with python code necessary to process results from the analysis.
2. file "pipeline-commands.txt": A text file summarizing the commands necessary for a genome-wide analysis for highly specific on-target sites. We provide notes at places where the genome and PAM sequences can be adjusted.

Website

Precomputed results for seven plant genomes can be found at https://www.genome.arizona.edu/crispr2/

The website also provides a detailed description of the analysis steps.

2018, Bastian Minkenberg