v3c-viz: Visualization and data exploration of chromosome conformation capture data at full resolution using Voronoi diagrams

Chromosome conformation capture (3C) sequencing approaches, like Hi-C or micro-C, allow for an unbiased view of chromatin interactions. Most analysis methods rely on so-called interaction matrices, which are derived from counting read pairs in bins of fixed size. To achieve high spatial resolution the general perception is that a high sequencing depth is required. Here, we show that high spatial resolution does not require high sequencing depth using the Voronoi diagram, as implemented in Voronoi for chromosome conformation capture data visualization (v3c-viz). The Voronoi diagram corresponds to an adaptive-binning strategy that adapts to the local densities of points. In this way, visualization of data obtained by moderate sequencing depth pinpoint many, if not most, interesting features such as high frequency contacts. The superior visualization properties of the Voronoi diagram calls for further developments towards algorithms for identifying contacts at a resolution approaching the typical size of enhancers and promoters.v3c-viz is available at https://github.com/imbbLab/v3c-viz