Ultrafast and accurate sequence alignment and clustering of viral genomes
Viromics produces millions of viral genomes and fragments annually, overwhelming traditional sequence comparison methods. Here we introduce Vclust, an approach that determines average nucleotide identity by Lempel-Ziv parsing and clusters viral genomes with thresholds endorsed by authoritative viral genomics and taxonomy consortia. Vclust demonstrates superior accuracy and efficiency compared to existing tools, clustering millions of genomes in a few hours on a mid-range workstation.
Authors
- Adam Gudyś (ORCID: https://orcid.org/0000-0002-5508-0090)
- Sebastian Deorowicz (ORCID: https://orcid.org/0000-0002-9496-733X)
- Andrzej Zieleziński (ORCID: https://orcid.org/0000-0002-8096-3776)
- Piotr Rozwalak (ORCID: https://orcid.org/0000-0002-4014-6624)
- Jakub Barylski (ORCID: https://orcid.org/0000-0001-6630-6932)
- Krzysztof Simiński (ORCID: https://orcid.org/0000-0002-6118-606X)
- Bas E. Dutilh (ORCID: https://orcid.org/0000-0003-2329-7890)
Institutions
- Silesian University of Technology (PL)
- Utrecht University (NL)
- Adam Mickiewicz University in Poznań (PL)
- Friedrich Schiller University Jena (DE)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-05-15
- DOI
- https://doi.org/10.1038/s41592-025-02701-7
- Citations
- 24
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 39.47
Funders
- Alexander von Humboldt-Stiftung
- Friedrich-Schiller-Universität Jena
- European Commission
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung
- Narodowym Centrum Nauki
- H2020 Marie Skłodowska-Curie Actions