The article introduces CRISPResso2, an updated version of the CRISPResso tool designed to facilitate the analysis of genome editing data from nucleases and base editors. CRISPResso2 offers several key innovations, including comprehensive analysis of base editor data, batch mode for comparing multiple experiments, allele-specific quantification of heterozygous or polymorphic references, a biologically-informed alignment algorithm, and ultra-fast processing time. The tool can quantify and visualize amplicon sequencing data, providing detailed reports and plots on base editing activity and nucleotide substitution frequencies. It also supports efficient processing of large datasets, improving accuracy and speed in analyzing indel events. The improved alignment algorithm ensures more accurate indel calling and reflects the current understanding of the editing mechanism. CRISPResso2 is available online and as a Docker image, making it accessible for researchers to analyze and compare genome editing experiments.The article introduces CRISPResso2, an updated version of the CRISPResso tool designed to facilitate the analysis of genome editing data from nucleases and base editors. CRISPResso2 offers several key innovations, including comprehensive analysis of base editor data, batch mode for comparing multiple experiments, allele-specific quantification of heterozygous or polymorphic references, a biologically-informed alignment algorithm, and ultra-fast processing time. The tool can quantify and visualize amplicon sequencing data, providing detailed reports and plots on base editing activity and nucleotide substitution frequencies. It also supports efficient processing of large datasets, improving accuracy and speed in analyzing indel events. The improved alignment algorithm ensures more accurate indel calling and reflects the current understanding of the editing mechanism. CRISPResso2 is available online and as a Docker image, making it accessible for researchers to analyze and compare genome editing experiments.