Skip to content

GVClass

GVClass assigns taxonomy to giant virus contigs and metagenome-assembled genomes (GVMAGs) by phylogenetic placement against giant virus orthologous groups (GVOGs). It covers Nucleocytoviricota (NCLDV), Mirusviricota, and the unified Preplasmiviricota (PPV), which groups virophages with Polinton-like viruses. Calls from domain through family are reliable. Genus and species are a nearest-reference label, not an ICTV assignment.

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. The contamination estimate is calibrated so the eukaryote-like genes giant viruses acquire by horizontal transfer do not count against a clean bin.

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 -b gvclass-dev 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/gvclass-dev/gvclass-a
chmod +x gvclass-a
./gvclass-a query results -t 32

For the full walkthrough, see Getting started.

Versions on this branch

Software 2.0.0, database bundle v1.7.1. 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, https://www.nature.com/articles/s44298-024-00069-7.

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