PEP compatible

geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA. When given one or more GEO/SRA accessions, geofetch will:

  • Download either raw or processed data from either GEO or SRA
  • Produces a standardized PEP sample annotation sheet of public metadata. This makes it really easy to run looper-compatible pipelines on public datasets by handling data acquisition and metadata formatting and standardization for you.

You can use it with the sra_convert pipeline, a pypiper pipeline that converts SRA files into BAM files.

Quick demo

geofetch runs on the command line. This command will download the metadata for the given GSE number.

geofetch -i GSE95654

You can add --just-metadata if you don't want to download the raw SRA files.

geofetch -i GSE95654 --just-metadata

For more details, check out the usage reference, installation instructions, or head on over to the tutorial for a detailed walkthrough.