CleanFinder: A Scalable Framework for Comprehensive Genome Editing Analysis

Precise validation of genome editing by targeted sequencing is a critical, multi-step process. Existing tools often separate amplicon definition from data analysis, creating fragmentation and added complexity. We developed CleanFinder, a browser-native application that unifies these steps. Based on user-provided sgRNAs or primers, CleanFinder retrieves the corresponding genomic context, automatically defines an amplicon, and sets robust sequence anchors. These anchors then guide alignment of sequencing reads, enabling accurate quantification of editing outcomes without relying on static, pre-loaded genome databases. Its analytical engine performs a comprehensive assessment of the sequencing data: it automates the classification of reads into key functional categories while simultaneously identifying heterozygous Single Nucleotide Polymorphisms (SNPs) to enable direct assessment of allelic dropout. To provide crucial biological context, the tool incorporates an interactive gene viewer that maps sgRNA targets and visualizes transcript-specific coding sequences, protein translations, and overall gene structure. Importantly, CleanFinder operates entirely client-side, ensuring complete data privacy as genomic information is never uploaded and no installation is required. By integrating these advanced analytical and visualization capabilities into a secure, all-in-one solution, CleanFinder makes robust genome editing analysis accessible to any researcher, regardless of their bioinformatics expertise.