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Downloads data and metadata from GEO and SRA and creates standard PEPs.

Project description

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PEP compatible Run pytests docs-badge pypi-badge Code style: black

geofetch is a command-line tool that downloads sequencing data and metadata from GEO and SRA and creates standard PEPs. geofetch is hosted at pypi. You can convert the result of geofetch into unmapped bam or fastq files with the included sraconvert command.

Key geofetch features:

  • Works with GEO and SRA metadata
  • Combines samples from different projects
  • Standardizes output metadata
  • Filters type and size of processed files (from GEO) before downloading them
  • Easy to use
  • Fast execution time
  • Can search GEO to find relevant data
  • Can be used either as a command-line tool or from within Python using an API

For more information, see complete documentation at geofetch.databio.org (source in the /docs folder).

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