Int J Biol Sci. 2018 May 22;14(8):858-862. doi: 10.7150/ijbs.24581. eCollection 2018.

You Q^1,2, Zhong Z³, Ren Q³, Hassan F³, Zhang Y³, Zhang T^1,2.

Abstract

Custom-designed nucleases, including CRISPR-Cas9 and CRISPR-Cpf1, are widely used to realize the precise genome editing. The high-coverage, low-cost and quantifiability make high-throughput sequencing (NGS) to be an effective method to assess the efficiency of custom-designed nucleases. However, contrast to standardized transcriptome protocol, the NGS data lacks a user-friendly pipeline connecting different tools that can automatically calculate mutation, evaluate editing efficiency and realize in a more comprehensive dataset that can be visualized. Here, we have developed an automatic stand-alone toolkit based on python script, namely CRISPRMatch, to process the high-throughput genome-editing data of CRISPR nuclease transformed protoplasts by integrating analysis steps like mapping reads and normalizing reads count, calculating mutation frequency (deletion and insertion), evaluating efficiency and accuracy of genome-editing, and visualizing the results (tables and figures). Both of CRISPR-Cas9 and CRISPR-Cpf1 nucleases are supported by CRISPRMatch toolkit and the integrated code has been released on GitHub (https://github.com/zhangtaolab/CRISPRMatch).

Key words: CRISPR; NGS data; automatic pipeline; genome-editing efficiency; mutation calculation

https://www.ncbi.nlm.nih.gov/pubmed/?term=CRISPRMatch%3A+An+Automatic+Calculation+and+Visualization+Tool+for+High-throughput+CRISPR+Genome-editing+Data+Analysis