Coxsackievirus A16 Nextstrain Analysis

This repository provides a comprehensive Nextstrain analysis of Coxsackievirus A16. You can choose to perform either a VP1 run (>=600 base pairs) or a whole genome run (>=6400 base pairs).
Live Nextstrain build can be found under VP1 or whole-genome.

For those unfamiliar with Nextstrain or needing installation guidance, please refer to the Nextstrain documentation.

Enhancing the Analysis

Most of the data for this analysis can be obtained from NCBI Virus. Instructions for downloading sequences are provided at the end of this README under Sequences.

Important

• All GitHub Actions "monthly runs" and their automatically generated commits live in the automatic-update branch.
• Inspect scheduled workflows or the generated commits on that branch: switch to automatic-update locally or view .github/workflows/ on that branch in the GitHub UI.
• If you are modifying scheduled automation, open PRs targeting automatic-update (unless you explicitly want changes applied to the default branch immediately).

Repository Organization

This repository includes the following directories and files:

• ingest: Contains Python scripts and the snakefile for automatic downloading of CVA16 sequences and metadata.
• scripts: Custom Python scripts called by the snakefile.
• snakefile: The entire computational pipeline, managed using Snakemake. Snakemake documentation can be found here.
• vp1: Sequences and configuration files for the VP1 run.
• whole_genome: Sequences and configuration files for the whole genome run.

Configuration Files

The config, vp1/config, and whole_genome/config directories contain necessary configuration files:

• colors.tsv: Color scheme
• geo_regions.tsv: Geographical locations
• lat_longs.tsv: Latitude data
• dropped_strains.txt: Dropped strains
• clades_genome.tsv: Virus clade assignments
• reference_sequence.gb: Reference sequence
• auspice_config.json: Auspice configuration file

The reference sequence used is G-10, accession number U05876.

Quickstart

Setup

Nextstrain Environment

Install the Nextstrain environment by following these instructions.

1. Generate reference files (one-time / when updating references)

   • Use helper to fetch GenBank-based reference files used by ingest:

     python3 ingest/generate_from_genbank.py --reference "U05876.1" --output-dir "whole_genome/config/"
     

   • For Enteroviruses, you'll get the CDS usually with: [0];[product];[2].
   • Output appears in data/references/ and is consumed by ingest rules.
   • Check data/references/pathogen.json attributes for correctness.

2. Run ingest (produces data/metadata.tsv and data/sequences.fasta)

   • Make vendored scripts executable if needed:

     chmod +x ./ingest/vendored/* ./ingest/bin/*
     

   • Run ingest via its Snakefile or via the main Snakefile:

     cd ingest
     snakemake all --cores 1
     

     or

     snakemake all --cores 1
     

     (See targets below for building specific outputs.)

3. Build specific Nextstrain outputs

   • VP1 (example target name — adapt to repo targets):

     snakemake  auspice/coxsackievirus_A16_vp1.json --cores 9
     

   • Whole genome:

     snakemake  auspice/coxsackievirus_A16_whole-genome.json --cores 9
     

4. Visualize locally with Auspice

   auspice view --datasetDir auspice
   

   • To run multiple views, change PORT:

     export PORT=4001
     

Notes & tips

• Snakemake targets: inspect the Snakefile to find exact auspice/ output filenames used in this repo.
• generate_from_genbank.py requires specifying feature/product indices used by the script — double-check the script CLI help if you see parsing errors.
• Keep automatic-update branch separate for scheduled workflows to avoid accidental merges from automation commits.

Sequences

• Manual: NCBI Virus (search CVA16 or Taxid 31704): https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/
• Automated: use the ingest pipeline (see repository ingest/ & vendored helpers).

Vendored scripts

• Vendoring is managed via git subrepo. To update vendored ingest scripts:
  • Install git-subrepo per its docs and follow instructions in ingest/vendored/README.md.

Contributing & maintenance

• For changes to scheduled automated updates: PR -> automatic-update.
• For code/pipeline/data changes: open PRs against the default branch (or discuss in issues first for large changes).
• For questions: open an issue or contact the maintainers.

References

• Nextstrain docs: https://docs.nextstrain.org/en/latest/
• Live build: https://nextstrain.org/groups/hodcroftlab/coxsackievirus/A16/vp1
• Reference sequence (G-10, U05876): https://www.ncbi.nlm.nih.gov/nuccore/U05876

Contact

• https://eve-lab.org/
• For data/pipeline queries: nadia.neuner-jehle[at]swisstph.ch