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GVClass

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. The taxonomy comes from a per-marker tree nearest-neighbor vote across the GVOG panels.

Where to go

  • Tutorials: learn GVClass by running it on the bundled example.
  • How-to guides: task recipes for bins, contigs, HPC, and tuning.
  • Reference: every flag, the 44 output columns, and config keys.
  • Explanation: how placement, taxonomy, and the quality models work.

Quick install

git clone https://github.com/NeLLi-team/gvclass.git
cd gvclass
pixi install
pixi run setup-db
pixi run example

wget https://raw.githubusercontent.com/NeLLi-team/gvclass/main/gvclass-a
chmod +x gvclass-a
./gvclass-a QUERY_DIR RESULTS_DIR -t 32

The wrapper pulls the library://nelligroup-jgi/gvclass/gvclass:2.0.0 Apptainer image and keeps the compact-resource warm cache under ~/.cache/gvclass/resource-cache/v2.0.0.

For the full walkthrough, see Getting started.

Current release

Software 2.0.0. pixi run setup-db downloads the public v2.0.0 resource archive from Zenodo and installs database DB_VERSION v2.0.0. Downloads and changelogs are on the GitHub Releases page.

Citation, license, contact

Cite Pitot et al. (2024), Conservative taxonomy and quality assessment of giant virus genomes with GVClass, npj Viruses.

Licensed under BSD-3-Clause. Questions and bugs go to GitHub Issues or fschulz@lbl.gov.