vConTACT

vConTACT assigns viral genomes to taxonomic groups using network-based analysis of whole-genome gene-sharing profiles to support virus taxonomy across archaeal and bacterial viruses, including uncultivated viruses.

Key Features:

• Network-Based Approach: Uses whole-genome gene-sharing profiles to construct gene-sharing networks representing relationships among viral genomes.
• Hierarchical Clustering and Confidence Scoring: Integrates distance-based hierarchical clustering and computes confidence scores for all taxonomic predictions to support genus-level assignments.
• Replication of Existing Taxonomies: Reproduces 96% of genus-level assignments from the International Committee on Taxonomy of Viruses for NCBI virus RefSeq.
• Scalability and Performance on Large Datasets: Assigned high-confidence genus labels to 820 of 1,364 previously unclassified RefSeq viruses and classified 31% of 15,280 Global Ocean Virome genome fragments in benchmark analyses.
• Applicability to Metagenomic Datasets: Applicable to and automatable for metagenomic datasets from diverse environments.

Scientific Applications:

• Virus Taxonomy: Provides a gene-sharing-based framework for classifying viral genomes to aid systematic taxonomy and studies of viral diversity and evolution.
• Metagenomic Analysis: Enables large-scale classification of viral genomes and genome fragments from environmental and host-associated metagenomic datasets, including ocean viromes.
• Research Automation: Supports automated workflows for high-throughput assignment of uncharacterized viral genomes to taxonomic groups.

Methodology:

Constructs gene-sharing networks from whole-genome gene-sharing profiles and applies distance-based hierarchical clustering with confidence scoring to assign genus-level taxonomy.