GVClass assigns taxonomy to giant virus genomes and metagenome-assembled genomes by phylogenetic placement against a comprehensive reference genome database. It covers Nucleocytoviricota (NCLDV), Mirusviricota, and Preplasmiviricota (PPV). It predicts taxonomy from domain down to genus and species level, assigning a nearest-reference label. Each genome returns a majority-vote taxonomy with a confidence flag, plus completeness and contamination metrics tuned for giant viruses.
Full documentation: https://NeLLi-team.github.io/gvclass/
- Tutorials — learn GVClass on the bundled example.
- How-to guides — bins, contigs, HPC, species trees, speed/accuracy, quality.
- Reference — every CLI flag, config key, output column, and marker panel.
- Explanation — how placement, taxonomy, and the quality models work.
Pixi (local):
git clone https://github.com/NeLLi-team/gvclass.git
cd gvclass
pixi install
pixi run setup-db
pixi run exampleApptainer (HPC):
wget https://raw.githubusercontent.com/NeLLi-team/gvclass/main/gvclass-a
chmod +x gvclass-a
./gvclass-a QUERY_DIR RESULTS_DIR -t 32The Apptainer image bundles the database and dependencies. See Getting started for the full walkthrough.
The wrapper pulls the library://nelligroup-jgi/gvclass/gvclass:2.0.0 SIF
from the public Sylabs library. The image embeds the compact v2.0.0 database
and writes its Parquet materialization cache to a host directory under
~/.cache/gvclass/resource-cache/v2.0.0.
GVClass works best on bins after metagenomic binning: a directory of one or more FASTA files (.fna or .faa), one file per putative genome. For giant virus discovery, filter contigs to >=30 kb (>=50 kb preferred). Use --min-length to adjust the MAG/bin nucleotide floor and --contigs with --contigs-min-length to classify each contig in a multi-contig .fna independently. Details are in the how-to guides.
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
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
The GVClass runtime resources include genomes and models derived from:
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/s41564-025-01906-2
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
BSD 3-Clause (see LICENCE). Report issues at https://github.com/NeLLi-team/gvclass/issues or contact fschulz@lbl.gov.