Download pre-built reference genome assets
refgenie command-line interface to download and organize genome assets. You do this by simply running
refgenie from the command line.
listr command lists remote assets to see what's available:
pull downloads the specific asset of your choice:
refgenie pull -g GENOME -a ASSET
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.
You can also browse and download pre-built refgenie assemblies manually at refgenomes.databio.org.