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 SRA or GEO
  • Produce a standardized PEP sample table. This makes it really easy to run looper-compatible pipelines on public datasets by handling data acquisition and metadata formatting and standardization for you.
  • Prepare a project to run with sraconvert to convert SRA files into FASTQ 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.