The other type was web services, such as Cas-analyzer, which had web GUI for online use, convenient for common users. Additionally, these command tools were often implemented for Unix-like operating systems, such as Linux, Unix or macOS, not compatible for Windows systems. These tools often came with command-line based usage, requiring the users had some bio-informatics experiences. One type was locally used, such as CRISPResso, CRIPSResso2 and CRISPR-DAV. They were categorized mainly into two types. To systematically analyze genome edits, currently several tools have been developed, including CRISPResso/CRISPResso2, Cas-analyzer, CRISPR-DAV, CRIS.py, and a few others (Table 1), which could accurately analyze certain kinds of genome editing events, but each has its limitations. We reasoned that an ideal bioinformatic program for analyzing CRISPR-mediated genome editing would feature: (1) user-friendly design with graphic user interface (GUI) to guide potential users throughout the process (2) easy installation in support of cross-platform usage (3) all-in-one solution to enable both single and multiple amplicon analysis and detection of base-editor mediated single nucleotide changes (4) locally deployed to avoid uploading of sensitive data or large NGS datasets (5) highly efficient and could finish whole-genome analysis within a reasonable time frame. Especially with the application of next-generation sequencing (NGS) and routine generation of large-scale datasets, systematic analysis of genome edits has become highly dependent on efficient bioinformatics tools. However, the off-target effect is still one of the major concerns for CRISPR-mediated genome editing experiments, and quantitative analysis of targeted/off-target indels has thus become a standard practice in the lab. Since its discovery, CRISPR has been widely used to understand basic biological processes and has been developed as a potential game-changer for therapeutic applications. When guided by a short gRNA transcript, CRISPR-Cas could be easily targeted to virtually any genomic loci and generate double-strand DNA breaks by recruiting cellular DNA repair machinery through either non-homologous end joining (NHEJ) or homology-directed repair (HDR), generating DNA insertion or deletion mutations (indels). CRISPR-GRANT source code is licensed under the GPLv3 license and free to download and use.ĬRISPR (clustered regularly interspaced short palindromic repeats) is a genome-editing technology derived from type II bacterial adaptive immune system, among which CRISPR/Cas9 and CRISPR/Cpf1 are the most widely used. CRISPR-GRANT binaries are freely available for Linux (above Ubuntu 16.04), macOS (above High Sierra 10.13) and Windows (above Windows 7) at. Therefore, CRISPR-GRANT is a valuable addition to the current CRISPR toolkits that significantly lower the barrier for wet-lab researchers to conduct indel analysis from large NGS datasets. Moreover, it also exhibited shorter run-time compared with tools currently available. CRISPR-GRANT offered a straightforward GUI by simple click-and-run for genome editing analysis of single or pooled amplicons and one-step analysis for whole-genome sequencing without the need of data pre-processing, making it ideal for novice lab scientists. Here, we developed CRISPR-GRANT, a stand-alone graphical CRISPR indel analysis tool, which could be easily installed for multi-platforms, including Linux, Windows, and macOS. Several indel analysis tools have been reported, however, it is often required that users have certain bioinformatics training and basic command-line processing capability. Indel analysis has thus become one of the most common practices in the lab to evaluate DNA editing events generated by CRISPR/Cas. CRISPR/Cas is an efficient genome editing system that has been widely used for functional genetic studies and exhibits high potential in biomedical translational applications.
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