Veritas Data

This repository contains the official datasets for Veritas, a tool for benchmarking and validating viral bioinformatics workflows.

Overview

The datasets stored here are curated to provide gold-standard data for validating variant calling and consensus generation pipelines. They include reference sequences, truth VCFs, primer schemes, and other metadata necessary for comprehensive benchmarking.

Dataset Structure

The datasets are organized by source, organism, and dataset name:

datasets/
└── source/ (e.g., veritas)
    └── organism/ (e.g., sars-cov-2)
        └── dataset_name/ (e.g., SEARCH-8113)
            ├── README.md           # Dataset documentation
            ├── metadata.yaml       # Dataset metadata
            ├── reference.fa        # Reference genome
            ├── truth.vcf.gz        # Truth variants (VCF)
            ├── primers.bed         # Primer scheme (optional)
            └── ...

Usage with Veritas

You can easily access and use these datasets using the Veritas CLI.

List Available Datasets

To see all available datasets:

veritas list-datasets

Download a Dataset

To download a specific dataset to your local machine:

veritas get-dataset \
  -d veritas/sars-cov-2/SEARCH-8113 \
  -o datasets

Run Validation

Once downloaded, you can use the dataset to validate your workflow results:

veritas validate \
  -d datasets/veritas/sars-cov-2/SEARCH-8113 \
  -q your_results.vcf.gz \
  -o validation_output

Contributing

We welcome contributions of new datasets! Please ensure your dataset includes:

1. Reference FASTA (reference.fa)
2. Truth VCF (bgzipped and indexed)
3. Metadata (metadata.yaml)
4. Documentation (README.md)
5. RTG SDF (rtg_sdf folder)
6. Primers (primers.bed, required for amplicon-seq datasets)

Please submit a Pull Request with your new dataset.