Ultrafast and accurate sequence alignment and clustering of viral genomes

Zielezinski, Andrzej; Gudys, Adam; Barylski, Jakub; Siminski, Krzysztof; Rozwalak, Piotr; Dutilh, Bas E.; Deorowicz, Sebastian

doi:10.1038/s41592-025-02701-7

Andrzej Zielezinski, Adam Gudys, Jakub Barylski, Krzysztof Siminski, Piotr Rozwalak, Bas E. Dutilh, Sebastian Deorowicz

Abstract:

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.

Reference:

Andrzej Zielezinski, Adam Gudys, Jakub Barylski, Krzysztof Siminski, Piotr Rozwalak, Bas E. Dutilh, Sebastian Deorowicz, Ultrafast and accurate sequence alignment and clustering of viral genomes, [in] Nature Methods, 2025, volume 22, number 6, pp. 1191-1194.

Bibtex Entry:

@Article{id:Zielezinski2025Ultrafast,  
	Author                   = "Zielezinski, Andrzej and Gudys, Adam and Barylski, Jakub and Siminski, Krzysztof and Rozwalak, Piotr and Dutilh, Bas E. and Deorowicz, Sebastian",  
	Title                    = "Ultrafast and accurate sequence alignment and clustering of viral genomes",  
	Journal                  = "Nature Methods",  
	Year                     = "2025",  
	Volume                   = "22",  
	Number                   = "6",  
	Pages                    = "1191-1194",  
	doi                      = "10.1038/s41592-025-02701-7",
	abstract                 = "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."
}