CRISPR-detector: fast and accurate detection, visualization, and annotation of genome-wide mutations induced by genome editing events

作者：Lei Huang, Dan Wang, Haodong Chen, Jinnan Hu, Xuechen Dai, Chuan Liu, Anduo Li, Xuechun Shen, Qi Chen, Hai‐Xi Sun, Dengwei Zhang, Tong Chen, Yuan Jiang · 发表于：Journal of genetics and genomics/Journal of Genetics and Genomics · 年份：2023 · DOI：10.1016/j.jgg.2023.03.010 · 被引用次数：10 · 研究领域：CRISPR and Genetic Engineering、Evolution and Genetic Dynamics、Plant Virus Research Studies

The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome editing. To track on/off-target events with emerging new editing techniques, improved bioinformatic tools are indispensable. Existing tools suffer from limitations in speed and scalability, especially with whole-genome sequencing (WGS) data analysis. To address these limitations, we have developed a comprehensive tool called CRISPR-detector, a web-based and locally deployable pipeline for genome editing sequence analysis. The core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline, with additional novel annotation and visualization modules designed to fit CRISPR applications. Co-analysis of the treated and control samples is performed to remove existing background variants prior to genome editing. CRISPR-detector offers optimized scalability, enabling WGS data analysis beyond Browser Extensible Data file-defined regions, with improved accuracy due to haplotype-based variant calling to handle sequencing errors. In addition, the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by users. These advantages facilitate rapid and efficient detection of mutations induced by genome editing events, especially for datasets generated from WGS. The web-based version of CRISPR-detector is available at https://db.cngb.org/crispr-detector, and the locally deployable v...