Nextstrain repository for Varicella-Zoster Virus (VZV)

Phylogenetic analysis of Varicella-Zoster Virus (VZV) using Nextstrain tools (Augur, Auspice, Nextclade, Snakemake)

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Repository structure

This repository contains three main workflows:

• ingest/ – Download and curate VZV data from GenBank and generate normalized metadata
• phylogenetic/ – Filter and align sequences, build the phylogenetic tree, assign clades and mutations, and export results for visualization.
• nextclade/ – Create a custom Nextclade dataset compatible with Nextstrain clade definitions and tree visualization
• check_sequences/ – Utilities and scripts to extract, compare and align duplicated genes (e.g. ORF62/71, ORF63/70, ORF64/69) and check the insertion for each sequence.

Each workflow directory (duplicated_genes_check/, phylogenetic/, nextclade/) contains its own README.md file with detailed documentation, including the purpose of the workflow, input/output files, configuration settings, and usage instructions.

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Installation

Follow the standard installation instructions for Nextstrain's suite of software tools.

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Quickstart

Run the phylogenetic workflow:

cd phylogenetic/
nextstrain build .
nextstrain view .

Or run the full ingest workflow:

cd ingest/
snakemake

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Documentation

• Running a pathogen workflow
• Creating a Nextclade dataset
• Auspice documentation