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3 Quick start

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Andrzej Zielezinski edited this page Oct 24, 2024 · 2 revisions

Follow these steps to quickly run Vclust on the provided example genomes. The process takes just a few seconds.

  1. Prefilter similar genome sequence pairs before conducting pairwise alignments.
vclust prefilter -i example/multifasta.fna -o fltr.txt
  1. Align similar genome sequence pairs and calculate pairwise ANI measures.
vclust align -i example/multifasta.fna -o ani.tsv --filter fltr.txt
  1. Cluster genome sequences based on given ANI measure and minimum threshold.
vclust cluster -i ani.tsv -o clusters.tsv --ids ani.ids.tsv --metric ani --ani 0.95

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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