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Adam Gudyś edited this page Oct 8, 2024 · 7 revisions

Welcome to the vclust wiki!

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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