OLIVE provides rapid visualization and analysis of chromatin tracing experiments

Optical chromatin tracing experiments directly capture the three-dimensional folding of thousands of individual alleles, highlighting the need for a tool that enables fast, interactive, and analytical browsing of such data. Here, we introduce optical looping interactive viewing engine (OLIVE), the first web-based application designed for high-throughput ball-and-stick chromatin tracing data studies that functions similarly to genome browsers. OLIVE allows users, regardless of computational expertise, to input their own data for automated reconstruction of chromatin fibers at individual alleles or to browse and analyze annotated publicly available datasets. Using OLIVE's functionalities, users can interact with three-dimensional presentation of traced alleles and query them based on spatial features, including pairwise distances and perimeters between their segments. Finally, OLIVE calculates and presents several polymer physics metrics of each allele, providing quantitative summaries for hypothesis-driven studies. OLIVE is an open-source project accessible at https://faryabilab.github.io/chromatin-traces-vis/.