Coxsackievirus A10 Nextstrain Analysis

This repository provides a comprehensive Nextstrain analysis of Coxsackievirus A10 (CVA10), suitable for both VP1 run (≥600 bp) and whole genome run (≥6400 bp) analyses.

For those unfamiliar with Nextstrain or needing installation guidance, see the Nextstrain documentation.

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Repository Organization

• ingest/: Python scripts and Snakefile for automatic downloading of CVA10 sequences and metadata (GenBank), formatting, and preparation.
• scripts/: Custom Python scripts called by the main Snakefile.
• snakefile: The main computational pipeline, managed using Snakemake. Snakemake docs
• vp1/: Sequences and configuration files for the VP1 run.
• whole_genome/: Sequences and configuration files for the whole genome run.
• data/: Static data files used by the workflow.

Configuration Files

The following files may be found under config/, vp1/config/, or whole_genome/config/:

• colors.tsv: Color scheme
• geo_regions.tsv: Geographical regions
• lat_longs.tsv: Latitude/longitude locations
• dropped_strains.txt: List of excluded strains
• clades_genome.tsv: Virus clade definitions/assignments
• reference_sequence.gb: Reference sequence (GenBank format)
• auspice_config.json: Auspice display config

⚠️ Note: The reference sequence used is Kowalik, accession number AY421767, sampled in 1950.

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Quickstart

1. Install Nextstrain

Follow instructions in the Nextstrain installation guide.

2. Data Preparation & Ingest Pipeline

CVA10 sequence and metadata ingestion is automated via the ingest/ workflow.

Prepare reference files:

• Check config/config.yaml and confirm taxid (NCBI) is correct.

• Run the reference extraction script:

  python3 ingest/bin/generate_from_genbank.py --reference "AY421767.1" --output-dir whole_genome/config/

  • The script may prompt for reference protein/CDS selection. Typical codes: [0] [product] [2].

• Ensure attributes in data/references/pathogen.json are up-to-date.

  • Reference: Nextclade pathogen config docs

Run the ingest workflow:

cd ingest
chmod +x ./vendored/*; chmod +x ./bin/*
snakemake --cores 4 all

This gathers/fetches and processes the latest public (and optionally, private) CVA10 sequence and metadata for downstream analysis.

3. Running a Build

In the project root:

snakemake --cores 9 all

Or, for a specific result:

• VP1:

  snakemake  auspice/coxsackievirus_A10_vp1.json --cores 9

• Whole genome:

  snakemake auspice/coxsackievirus_A10_genome.json --cores 9

4. Visualizing

To view build results in Auspice:

auspice view --datasetDir auspice

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Data Input

• Automatic: The ingest/ pipeline fetches up-to-date public data. Private sequences or metadata (e.g. new submissions) can be incorporated by adding to data/meta_manually_added.tsv.
• Manual: Download from NCBI Virus, searching for “CVA10” or Taxid.

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Updating Vendored Scripts

This repository uses git subrepo to manage ingest scripts in ingest/vendored. To update:

git subrepo pull ingest/vendored

See details in ingest/vendored/README.md.

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Troubleshooting & Notes

• Reference collection date/inclusion: Make sure the true collection date for the reference sequence is in your metadata to avoid downstream tree artifacts.
• Colors: If not found in Auspice, make sure your auspice_config.json does include them.

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Feedback

For questions or comments, please contact us per e-mail (eve-group[at]swisstph.ch) or open an issue.

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For advanced users and further workflow options, see the documentation in each subdirectory (especially ingest/README.md).