PanDora: Pangenome Database of Reference Assemblies

A non-redundant human pangenome database for microbiome sequence decontamination using reference assemblies.

Overview

The create-pandora script constructs a non-redundant human pangenome database by combining standard reference genomes (GRCh38, CHM13-T2T) with Human Pangenome Reference Consortium (HPRC) graph-based sequences. The resulting database (PanDora) enables sensitive detection of human DNA contamination in sequencing datasets and provides a comprehensive reference for alignment-based analyses.

This database integrates genomes from the following projects:

• The Genome Reference Consortium human reference assembly, GRCh38 (NCBI RefSeq GCF_000001405.40)
• The T2T Consortium human reference assembly, CHM13v2.0 (NCBI RefSeq: GCF_009914755.1)
• The Human Pangenome Reference Consortium (HPRC) Year 1 assemblies (available on GitHub or NCBI; PRJNA730823)

Quick Start

# Clone repository with dependencies
git clone --recursive https://github.com/promicrobial/pandora.git
cd pandora

# Install dependencies
conda env create -f environment.yml
conda activate pandora

# Create database (requires HPRC GFA file)
./create-pandora -g /path/to/hprc.gfa -o pandora_db -v

Installation

Requirements

The following tools must be installed and available in your PATH:

• bash (version 4+)
• Standard Unix tools (e.g. gunzip)
• panSieve (GitHub)
• seqtk v1.5
• NCBI datasets CLI v18.15.0

# Install dependencies using conda
conda env create -f environment.yml

# Clone panSieve and add to your PATH
git clone https://github.com/cpnh/panSieve

export PATH="panSieve/src/:$PATH"

Usage

To recreate the database

create-pandora -g ref/hprc-v1.0-minigraph-grch38.gfa

Command Line Options

Option	Description	Default
-g, --gfa FILE	Required: Path to HPRC GFA file	-
-o, --output DIR	Output directory	./pandora_output
-t, --threads NUM	Number of threads	4
-f, --force	Force recreation of existing files	false
-v, --verbose	Enable verbose logging	false
-k, --keep-temp	Keep temporary files	false
-d, --dry-run	Show commands without executing	false
-h, --help	Show help message	-
--version	Show version information	-

Input Requirements

HPRC GFA File

Download from the Human Pangenome Reference Consortium:

# Example: Download and unzip HPRC GFA file
wget -q -O- ftp://ftp.sra.ebi.ac.uk/vol1/analysis/ERZ127/ERZ12792760/hprc-v1.0-minigraph-grch38.gfa.gz | gzip -d > hprc-v1.0-minigraph-grch38.gfa

Documentation

Full documentation is available in the docs directory.

License

This project is licensed under the MIT License - see the LICENSE file for details.