Variant-aware Cas-OFFinder: web-based <i>in silico</i> variant-aware potential off-target site identification for genome editing applications

Genome editing based on CRISPR systems has been widely used in the vast areas of biomedical and agricultural applications. However, identifying the potential off-target sites remains challenging, particularly in individuals with diverse genetic variations. Several in silico tools have been developed to predict potential off-target sites, but they have limitations on their performance and scalability. In this paper, we present "Variant-aware Cas-OFFinder," a novel pipeline based on Cas-OFFinder for identifying potential off-target sites by accounting for individual genetic variants. We benchmarked the pipeline's improved scalability and performance with the human genome and pepper cultivars, having unique potential off-target sites on each allele at the haplotype level. The web tool is open to all users without a login requirement and is freely available online at https://rgetoolkit.com/var-cas-offinder.