OffRisk: a docker image for annotating CRISPR off-target sites in the human genome

Gil-Ad Barkai; Tal Malul; Yossi Eliaz; Eran Eyal; Isana Veksler-Lublinsky

doi:10.1093/bioadv/vbad138

OffRisk: a docker image for annotating CRISPR off-target sites in the human genome

Bioinform Adv. 2023 Oct 6;3(1):vbad138. doi: 10.1093/bioadv/vbad138. eCollection 2023.

Authors

Gil-Ad Barkai¹, Tal Malul¹, Yossi Eliaz^{2

3

4}, Eran Eyal⁵, Isana Veksler-Lublinsky¹

Affiliations

¹ Department of Software & Information Systems Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
² Computer Science Department, HIT Holon Institute of Technology, Holon, Israel.
³ Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
⁴ NRGene LTD, Rehovot, Isarel.
⁵ Evogene LTD, Rehovot, Isarel.

Abstract

Summary: The CRISPR-Cas9 system has been adapted to achieve targeted genome editing as well as transcriptional control by customizing 20-nt guide RNA (gRNA) molecules for desired regions in the target genome. Designing gRNAs must consider nonspecific and unintended binding, known as off-targets, since these may have potentially harmful effects. To assist in gRNA design, we have developed OffRisk. This Docker-based tool annotates off-target sites in the human genome and assigns them a potential risk label by incorporating functional and regulatory information at different molecular levels.

Availability and implementation: OffRisk is available at https://github.com/IsanaVekslerLublinsky/OffRisk and https://github.com/IsanaVekslerLublinsky/OffRisk-ui (including code, user guide, docker installation guide, and running examples).All processed datasets are available at https://zenodo.org/record/8289271.