Genome reference downloader

SOPRANO has a built-in genome reference downloader, that retrieves data directly from the Ensembl ftp servers. This means that SOPRANO users do not need to configure VEP, for example.

Users can execute the utility via

soprano-get-genome [-h] [--species SPECIES] [--assembly ASSEMBLY] [--release RELEASE] [--primary_assembly] [--download_only]

-h | --help

Get info on how to use this executable

-s | --species

Ensembl species Latin name. (default: homo_sapiens)

-a | --assembly

Ensembl genome assembly ID. (default: GRCh38)

-r | --release

Ensembl release number. (default: 110)

-d | --download_only

Don't decompress and compute fasta index file.

Downloads will be cached into the folder ensembl_downloads/SPECIES/RELEASE. This mimics the VEP downloads structure. This is deliberate: users who readily have genome references downloaded on their local laptop can leverage the soprano-link-vep utility to crete a soft link to existing data in this directory, which can then be used by SOPRANO.