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 -g GENOME -a 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 -g hg38 -a bowtie2_index

You can also pull many assets at once:

refgenie pull --genome mm10 --asset bowtie2_index hisat2_index

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

That's it! Easy.

Downloading manually

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