GVClass

GVClass classifies giant-virus genomes and metagenome-assembled genomes using marker-gene trees. It supports Nucleocytoviricota (NCLDV), Mirusviricota and Preplasmiviricota (PPV), and reports taxonomy, marker counts, completeness and contamination estimates.

Install and run

On Linux x86-64 with Pixi and Git installed:

git clone https://github.com/NeLLi-team/gvclass.git
cd gvclass
pixi install --frozen
pixi run setup-db
pixi run gvclass example -o example_results -t 8
head -n 4 example_results/gvclass_summary.tsv

Create a directory for your genomes:

mkdir -p query_genomes

Put one genome per .fna file or one proteome per .faa file in this directory, then run:

pixi run gvclass query_genomes -o results -t 8

To build a shared species tree as well:

pixi run gvclass query_genomes -o species_tree_results -t 8 --species-tree-combined

Documentation

• Getting started: installation, bundled examples and output.
• Classify genome bins: input preparation and resume.
• Build a species tree: per-query and combined trees.
• Run on a cluster: Slurm and Apptainer.
• Command-line options and output columns.
• Methods: taxonomy and quality estimates.

Citation

Pitot et al. (2024): Conservative taxonomy and quality assessment of giant virus genomes with GVClass. npj Viruses. https://www.nature.com/articles/s44298-024-00069-7

Database sources

The trained contamination model is shipped in the runtime resource bundle at resources/contamination/model.joblib.

The v2.0.0 runtime resource bundle is archived on Zenodo: https://doi.org/10.5281/zenodo.21225457

Reference data sources:

Medvedeva S, Guyet U, Pelletier E, et al. (2026): Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes. Nature Microbiology 11:228-239. https://doi.org/10.1038/s41564-025-02190-6

Roux S, Fischer MG, Hackl T, Katz LA, Schulz F, Yutin N (2023): Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 13(2):204. https://doi.org/10.3390/biom13020204

Fiamenghi MB, Camargo AP, Chasapi IN, et al. (2025): Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes. Nucleic Acids Research gkaf1283. https://doi.org/10.1093/nar/gkaf1283

Vasquez YM, Nardi T, Terasaki GM, et al. (2025): Genome-resolved expansion of Nucleocytoviricota and Mirusviricota reveals new diversity, functional potential, and biotechnological applications. bioRxiv 2025.09.26.678796. https://doi.org/10.1101/2025.09.26.678796

Bellas CM, Sommaruga R (2026): A framework for Polinton-like virus diversity across aquatic microbiomes reveals links to multiple viral classes and Nucleocytoviricota. bioRxiv 2026.06.19.733378. https://doi.org/10.64898/2026.06.19.733378

License and contact

Non-commercial use only (see LICENCE). Report issues at https://github.com/NeLLi-team/gvclass/issues or contact fschulz@lbl.gov.