ArticleCurrent protocols2026
Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.
Article in Current protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.Current protocols · 2026Article
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Authors and funding
3 authors.
Funding
Abstract
Metagenomic Hi-C (metaHi-C) links mobile genetic elements to their cellular hosts directly within complex microbial communities. Once shotgun and Hi-C libraries have been generated, however, the main challenges shift to the bioinformatics required for preprocessing, genome binning, taxonomic annotation, and network-level interpretation. Here, we present metaHi-C protocols that span from raw reads to downstream data analyses. Basic Protocol 1 describes quality control of shotgun and Hi-C reads, metagenomic assembly, Hi-C read mapping, and viral contig identification from assembled contigs. Basic Protocol 2 details the use of ViralCC to recover viral metagenome-assembled genomes (vMAGs) and infer virus-host linkages. Support Protocol 1 introduces NormCC and ImputeCC for normalization of raw Hi-C contacts and host genome binning. Support Protocols 2 and 3 describe taxonomic annotation of host MAGs with GTDB-Tk and viral bins with Virgo, respectively. Support Protocol 4 shows how to integrate these outputs in MetaHiCNet to generate cross-taxa and cross-bin Hi-C interaction networks. Together, these protocols provide a reproducible workflow for reconstructing viral and host genomes, assigning consistent taxonomies, and visualizing metaHi-C-derived virus-host interaction structure across diverse microbiomes. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preprocessing raw metagenomic Hi-C data Basic Protocol 2: Viral genome binning and virus-host interaction inference using ViralCC Support Protocol 1: Host genome binning using ImputeCC Support Protocol 2: Host MAG taxonomic annotation with GTDB‑Tk Support Protocol 3: Viral bin taxonomic annotation with Virgo Support Protocol 4: Visualization of virus-host interaction networks with MetaHiCNet.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.