Efficient querying of genomic reference databases with gget

Abstract

MotivationA recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. Currently, there is no tool implementing automated, easy programmatic access to curated reference information stored in a diverse collection of large, public genomic databases. Resultsgget 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. AvailabilityThe manual and source code are available at https://github.com/pachterlab/gget. Contactlpachter@caltech.edu