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Andrzej Zielezinski edited this page May 19, 2025 · 8 revisions

Vclust logo Vclust User Guide

Vclust is an alignment-based tool for fast and accurate calculation of Average Nucleotide Identity (ANI) between complete or metagenomically-assembled viral genomes. The tool also performs ANI-based clustering of genomes according to standards recommended by international virus consortia, including International Committee on Taxonomy of Viruses (ICTV) and Minimum Information about an Uncultivated Virus Genome (MIUViG).

Citation

Zielezinski A, Gudyś A, Barylski J, Siminski K, Rozwalak P, Dutilh BE, Deorowicz S. Ultrafast and accurate sequence alignment and clustering of viral genomes. Nature Methods. 2025 [doi:10.1038/s41592-025-02701-7].

License

GNU General Public License, version 3

Table of contents

Vclust User Guide

  1. Features
  2. Installation
  3. Quick Start
  4. Usage
    1. Input data
    2. Prefilter
    3. Align
    4. Cluster
    5. Deduplicate
  5. Optimizing sensitivity and resource usage
    1. Prefilter
  6. Use cases
    1. Classify viruses into species and genera following ICTV standards
    2. Assign viral contigs into vOTUs following MIUViG standards
    3. Dereplicate viral contigs into representative genomes
    4. Calculate pairwise similarities between all-versus-all genomes
    5. Deduplicate (remove identical sequences) across multiple datasets
    6. Process large dataset of diverse virus genomes (IMG/VR)
    7. Process large dataset of highly redundant virus genomes
    8. Cluster plasmid genomes into pOTUs
  7. FAQ: Frequently Asked Questions
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