CleanFinder: Browser-Native Analysis of Editing Outcomes and Allelic States

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 into a single, streamlined workflow.

Based on user-provided sgRNAs or primer pairs, CleanFinder retrieves the corresponding genomic context and automatically defines the amplicon region, allowing users to copy or visualize the targeted sequence. When sgRNAs are supplied, they also establish sequence anchors that guide the alignment of sequencing reads for accurate quantification of editing outcomes. These anchors are fully adjustable, enabling users to extend or contract upstream and downstream regions as needed. The analytical engine then classifies sequencing reads into key functional categories, while a dedicated allelic dropout module identifies heterozygous single-nucleotide polymorphisms (SNPs) to support direct assessment of allelic dropout events.

To provide essential biological context, CleanFinder includes 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 since genomic information is never uploaded and no installation is required. By integrating advanced analytical and visualization capabilities into a secure, all-in-one solution, CleanFinder makes robust genome editing analysis accessible to any researcher, regardless of bioinformatics expertise.