Metadata retrieval from sequence databases with ffq

Abstract

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. Availability and implementation ffq is free and open source, and the code can be found here: https://github.com/pachterlab/ffq.