OC43 Ingest and Analysis Pipeline

This repository provides a complete ingest and analysis pipeline for Human coronavirus OC43 (HCoV-OC43), built using Snakemake and based on the Nextstrain framework.

It includes tools to download and process OC43 sequences and metadata, generate Nextstrain-compatible inputs, and perform genomic analysis and visualization.

The data for this analysis is available from NCBI Virus. Instructions for downloading sequences are provided under Sequences.

Prerequisites

Ensure the following are installed:

• Python=3.8 or higher
• Micromamba or Conda
• Snakemake=7
• Nextstrain CLI

Installation

Install the Nextstrain environment by following these instructions.

Sequences

You can download OC43 sequences:

Manually from NCBI Virus

Automatically using the ingest pipeline. Please refer to the README in the ingest folder.

Configuration Files

Found in config and data subdirectories:

config.yaml: Pipeline configuration

geo_regions.tsv, lat_longs.tsv: Geographical mappings

colors.tsv: Color palette for Nextstrain builds

clades_genome.tsv: For manually labeling clades

dropped_strains.txt: List of strains to exclude

auspice_config.json: Required for visualization

reference_sequence.gb: Reference file for OC43 (from GenBank: AY391777)

Nextstrain Analysis

You can perform either a whole-genome or protein-specific build of OC43 using Nextstrain.

Usage Examples

Activate your environment:

micromamba activate nextstrain

Run a full build:

snakemake --cores 9 all

Run specific builds:

snakemake auspice/HCoV_OC43_genexy.json --cores 9
snakemake auspice/HCoV_OC43_whole_genome.json --cores 9

Visualizing the Build

auspice view --datasetDir auspice

To run two visualizations simultaneously, you may need to set the port:

export PORT=4001

🙏 Acknowledgments

• Nextstrain
• Auspice
• Hodcroftlab
• Snakemake
• Biopython
• Genbank
• NCBI

📬 Contact For questions or support, please contact: nosihle.msomi@swisstph.ch