Journal
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
Volume 14, Issue 8, Pages 858-862Publisher
IVYSPRING INT PUBL
DOI: 10.7150/ijbs.24581
Keywords
CRISPR; NGS data; automatic pipeline; mutation calculation; genome-editing efficiency
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Funding
- Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)
- Sichuan Youth Science and Technology Foundation [2017JQ0005]
- National Science Foundation of China [31771486]
- Fundamental Research Funds for the Central Universities [ZYGX2016J119]
- Jiangsu Specially-Appointed Professor
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Custom-designed nucleases, including CRISPR-Cas9 and CRISPR-Cpfl, 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-Cpfl nucleases are supported by CRISPRMatch toolkit and the integrated code has been released on GitHub (https://github.com/zhangtaolab/CRISPRMatch).
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