Protocol for comprehensive genotyping of nuclease, base, and prime editing outcomes using CleanFinder

Genome editing experiments often produce heterogeneous allele mixtures that require structured genotyping. Here, we present a protocol for analyzing amplicon sequencing data from nuclease, base, prime, and mitochondrial base editing experiments using CleanFinder. We describe steps for preparing reference sequences and FASTQ files and running browser-native or command-line analyses. We then detail interpretation of genotype distributions, repair signatures, editing efficiencies, and allelic dropout. For complete details on the use and execution of this protocol, please refer to Ramachandran et al.¹ and cleanfinder.org.