Efficient querying of genomic reference databases with gget

• DOI: 10.1093/bioinformatics/btac836
• Publication Date: 2023-01-08T03:22:39Z
• Authors: Laura Luebbert; Lior Pachter
• Keywords: Statistics and Probability; Data Analysis; 0301 basic medicine; 570; 0303 health sciences; Genome; Databases, Factual; Genomics; Biochemistry; Computer Science Applications; 004; Computational Mathematics; Applications Note; 03 medical and health sciences; Computational Theory and Mathematics; Molecular Biology; Software

Abstract

Motivation A recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. With the increasing number of command line and Python users, there is a need for tools implementing automated, easy programmatic access to curated reference information stored in a diverse collection of large, public genomic databases.

Results gget is a free and open-source command line tool and Python package that enables efficient querying of genomic reference databases, such as Ensembl. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying required for genomic data analysis in a single line of code.

Availability and implementation The manual and source code are available at https://github.com/pachterlab/gget.

Supplementary information Supplementary data are available at Bioinformatics online.