<b>A comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies</b>

Chromatin Conformation Capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions And the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions mediated by a protein of interest with high specificity. To analyze these large and complex datasets, computational methods are undergoing a rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to establish which commonly used algorithms and processing pipelines need to be improved. To deepen the interpretation of targeted conformation capture data, and expedite the development of computational methods, we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods, and provide practical recommendations for users working with HiChIP and/or ChIA-PET analysis.