Metadata retrieval from sequence databases with ffq

Abstract

Motivation: Several genomic databases host data and metadata for an ever-growing collection of sequence datasets. While these databases have a shared hierarchical structure, there are no tools specifically designed to leverage it for metadata extraction. Results: We present a command-line tool, called ffq, for querying user-generated data and metadata from sequence databases. Given an accession or a paper’s DOI, ffq efficiently fetches metadata and links to raw data in JSON format. ffq’s modularity and simplicity make it extensible to any genomic database exposing its data for programmatic access.