PanDora: Pangenome Database of Reference Assemblies

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

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)

Contents

• Number of assemblies used: 94
• Total size: 9.6 GB
• File format: FASTQ

To recreate the database

Requirements

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

• datasets (NCBI datasets CLI)
• panSieve (GitHub)
• seqtk
• seqkit
• vg
• bcftools
• tabix
• bgzip

# 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

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

Documentation

Full documentation is available in the docs directory.

License

MIT