Efficient querying of genomic reference databases with gget

Abstract

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.