Download pre-built reference genome assets

Introduction

Use the refgenie command-line interface to download and organize genome assets. You do this by simply running refgenie from the command line.

The listr command lists remote assets to see what’s available:

refgenie listr

The pull downloads the specific asset of your choice:

refgenie pull GENOME/ASSET

Where GENOME refers to a genome key (e.g. hg38) and ASSET refers to one or more specific asset keys (e.g. bowtie2_index). For example:

refgenie pull hg38/bowtie2_index

Pull multiple assets

You can pull several assets in one command by listing them as positional arguments:

refgenie pull hg38/bowtie2_index hg38/bwa_index mm10/fasta

Batch pulling with --genome

To pull all available assets for a specific genome, use the --genome flag combined with --all:

refgenie pull --genome hg38 --all

This downloads every asset available on the server for the hg38 genome. You can also pull all assets across all genomes:

refgenie pull --all --all-genomes

Controlling large asset downloads

Some assets are very large. Refgenie provides flags to control how large assets are handled:

Flag	Description
--skip-large	Skip assets larger than the size cutoff without prompting
--large	Download large assets without prompting
--size-cutoff	Size threshold in bytes (assets above this are “large”)
--batch	Non-interactive mode: apply the large/skip-large policy without prompting

For example, to pull all assets but skip anything over 1 GB:

refgenie pull --genome hg38 --all --skip-large --size-cutoff 1073741824 --batch

Initialize genome on pull

If you are pulling an asset for a genome that has not been initialized locally, use the --init flag to automatically initialize the genome:

refgenie pull hg38/fasta --init

Force re-download

To re-download an asset that already exists locally, use the --force flag:

refgenie pull hg38/fasta --force

Skipping specific asset classes or recipes

You can exclude certain asset classes or recipes from batch pulls:

refgenie pull --genome hg38 --all --skip-asset-class star_index
refgenie pull --genome hg38 --all --skip-recipe star_index

Error handling

If a pull fails (e.g., network error, asset not found on server), refgenie logs a warning and continues with the remaining assets. Check the log output for details about any failures.

Common issues:

• “No local digest for genome alias”: The genome alias is not yet known locally. Refgenie will attempt to resolve it with the server automatically, or you can use --init.
• Server unreachable: Verify your server subscription with refgenie config get and check your network connection.
• Asset not found: Use refgenie listr to verify the asset exists on the server.

To see more details, consult the usage docs by running refgenie pull --help.

Downloading manually

You can also browse and download pre-built refgenie assemblies manually at refgenomes.databio.org.