CRISPR-Detector: Fast and Accurate Detection, Visualization, and Annotation of Genome Wide Mutations Induced by Gene Editing Events

The leading edge of genome editing, driven especially by CRISPR/Cas technology, is revolutionizing life sciences. In pace with the burst of novel genome editing methods, bioinformatic tools to monitor the on/off-target events need to be more accurate and capable of detecting true editing-induced mutations. Existing tools suffer from limitations in speed and scalability, especially struggle in the whole genome sequencing data analysis which is believed to replace amplicon sequencing and become mainstream data type due to the rapidly decreasing sequencing cost. Here, we introduce our CRISPR-detector tool, which is either a web-hosted or locally deployable pipeline with five key innovations: 1) optimized scalability allowing for whole genome sequencing data analysis beyond BED file-defined regions; 2) improved accuracy benefited from haplotype based variant calling to handle sequencing errors; 3) treated and control sample co-analysis to remove background variants existing prior to genome editing; 4) integrated structural variation (SV) calling with additional focus on vector insertions from viral-mediated genome editing; 5) functional and clinical annotation of editing-induced mutations. ### Competing Interest Statement The authors have declared no competing interest.