Dataset Configuration

ViralQC uses a configuration file called datasets.yml to define which viruses and datasets are available for analysis. This file is located at viralqc/config/datasets.yml.

datasets.yml File Structure

The file has two main sections:

nextclade_data: Datasets hosted in the official Nextclade repository
github: Custom datasets hosted on GitHub

nextclade_data:
  virus-identifier:
    dataset: "dataset/path"
    tag: "dataset-version"
    virus_name: "Virus Name"
    # ... other parameters

github:
  virus-identifier:
    repository: "user/repository"
    dataset: "dataset/path"
    tag: "development"
    virus_name: "Virus Name"
    # ... other parameters

Nextclade Datasets

Nextclade datasets are official or community datasets available through the nextclade_data repository.

nextclade_data:
  denv1:
    dataset: "community/v-gen-lab/dengue/denv1"
    tag: "2025-04-02--19-11-08Z"
    virus_name: "Dengue virus type 1"
    virus_tax_id: 11053
    virus_species: "Orthoflavivirus denguei"
    virus_species_tax_id: 3052464
    segment: "Unsegmented"
    ncbi_id: "NC_001477.1"
    target_gene: "E"
    target_regions: ["C", "prM", "E"]
    private_mutation_total_threshold: 70

GitHub Datasets

Custom datasets can be hosted in GitHub repositories.

github:
  zikav:
    repository: "dezordi/nextclade_data_workflows"
    dataset: "zikaV/dataset"
    tag: "development"
    virus_name: "Zika virus"
    virus_tax_id: 64320
    virus_species: "Orthoflavivirus zikaense"
    virus_species_tax_id: 3048459
    segment: "Unsegmented"
    ncbi_id: "NC_035889.1"
    target_gene: "E"
    target_regions: ["C", "prM", "E"]
    private_mutation_total_threshold: 40

Configuration Parameters

Parameter	Type	Description
`dataset`	String	Dataset path in nextclade_data or GitHub repositories
`repository`	String	GitHub repository name in `user/repo` format (for `github`)
`tag`	String	Dataset version/tag or repository branch
`virus_name`	String	Full virus name
`virus_tax_id`	Integer	Virus taxonomic ID in NCBI Taxonomy
`virus_species`	String	Viral species name
`virus_species_tax_id`	Integer	Species taxonomic ID
`segment`	String	Segment name (use “Unsegmented” for non-segmented viruses)
`ncbi_id`	String	Reference genome accession in NCBI
`target_gene`	String	Target gene/CDS name
`target_regions`	List	List of target genes/CDS
`private_mutation_total_threshold`	Integer	Private mutation threshold for quality control

Note

For non-segmented viruses (e.g., Dengue, Zika, SARS-CoV-2), use "Unsegmented" for the segment field. For segmented viruses, specify the segment name (e.g., "HA", "NA", "L", "M", "S").