MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks

Metagenomic Hi-C (metaHi-C) enables the reconstruction of microbial genome organization and interspecies interactions by capturing physical contacts between genomic fragments. However, raw metaHi-C data are often confounded by systematic biases and spurious contacts, which can obscure meaningful biological signals. Existing metaHi-C pipelines typically lack user-friendly normalization workflows and intuitive visualization tools, limiting the ability to explore microbial interaction networks. Here, we introduce MetaHiCNet, a web-based platform that supports widely used normalization methods with customizable parameters. MetaHiCNet provides a stepwise workflow for bias correction, spurious contact removal, and interactive visualization of microbial interactions. The platform supports multiple visualization modes, including taxonomic treemaps, cross-taxa networks, and cross-bin networks, enabling seamless transitions from community-wide overviews to detailed analyses of specific taxa or bins. This functionality facilitates the investigation of host-microbe interactions and the relationships between mobile genetic elements and their microbial hosts, offering deeper insights into microbial community structures and dynamics. MetaHiCNet is freely accessible at www.metahicnet.com without login.