| name | vcontact |
| description | vConTACT2 / vConTACT3 — gene-sharing network and ML-based hierarchical virus taxonomy for prokaryotic (and in v3, broader realm) viral genomes/contigs. Use after viral discovery (geNomad / VirSorter2) and quality (CheckV): (1) Genus-to-order style clustering, (2) Placing vMAGs vs RefSeq/ICTV, (3) Choosing v2 vs v3. Upstream: https://bitbucket.org/MAVERICLab/vcontact2 and https://bitbucket.org/MAVERICLab/vcontact3.
|
| license | MIT |
| category | analysis-tools |
| tags | ["virus","taxonomy","vConTACT","gene-sharing","ICTV"] |
| upstream | https://bitbucket.org/MAVERICLab/vcontact3 |
| stage | mining |
vConTACT2 / vConTACT3
Upstream: vConTACT2 ·
vConTACT3
Citation
Jang, H. B. et al. Taxonomic assignment of uncultivated prokaryotic virus
genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632–639
(2019). https://doi.org/10.1038/s41587-019-0100-8
Bolduc, B. et al. Machine learning enables scalable and systematic hierarchical
virus taxonomy. Nat. Biotechnol. (2025).
https://doi.org/10.1038/s41587-025-02946-9
See also docs/references.md.
Analytical thinking
Viruses lack a universal marker gene. vConTACT builds gene-sharing networks
(v2) and, in v3, ML hierarchical taxonomy with realm-aware cut-offs, scaling
to large metagenomic viral sets and improving agreement with ICTV-style ranks.
Pipeline position:
contigs → genomad | virsorter2 → checkv (quality filter)
→ proteins (Prodigal/Bakta as required by vConTACT)
→ vcontact3 (prefer for new work) | vcontact2
| Edition | Prefer when |
|---|
| vConTACT3 | New analyses; hierarchical ranks; broader realms; scale |
| vConTACT2 | Reproducing older Methods / published networks |
Network clusters ≠ wet-lab host range. Report reference DB (Viral RefSeq /
ICTV snapshot) and software version.
How to run
Decision tree
Viral sequences in hand?
├─ Not yet discovered → genomad / virsorter2
├─ Need quality → checkv
├─ Need taxonomy / clustering → vcontact (v3 preferred)
└─ Only presence of viral contigs → stop at genomad/checkv
Related skills
genomad · virsorter2 · checkv · microbial-mining · prodigal ·
tool-selection
