Crispy: A Tool to Assess CRISPR-Mediated Genome Editing

Next generation sequencing (NGS) is widely used to evaluate the accuracy of gene editing with CRISPR-Cas9, and the analysis of these sequencing experiments requires dedicated bioinformatic tools. Most of the web-based algorithms focus on the frequency of correction rather than providing a detailed outcome of the experiment. On the other hand, command line tools usually provide more details, but they are not easily accessible to researchers that are not experts in bioinformatics. In order to combine detailed outcomes with easy-to-use, we implemented a self-contained python module with a graphical user interface for the analysis of gene editing experiments. CRISPY first aligns NGS reads against the reference genome using the Burrows Wheeler Alignment. Reads are compared to the reference genome in a range of interest surrounding the target position. The comparison with the reference genome is used to calculate the number of identical sequences, synonym sequences and indels induced by the nucleases. The indel frequency is calculated by dividing indels by the total number of reads while the percent of wild type allele by dividing the identical sequences plus synonymous sequences mutations by the total number of reads. The percentage of correction is calculated as the fraction of mutated alleles in the control sample that is corrected to the wild type allele in the treated sample. In order to estimate the robustness of the estimated value for the percentage of correction, 1000 datasets are generated by bootstrapping from the experimental reads in the control and treated samples. The percentage of correction is calculated for each bootstrapped dataset, and the 95 confidence intervals are estimated.