RT Journal Article
SR Electronic
T1 Efficient querying of genomic reference databases with <em>gget</em>
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.05.17.492392
DO 10.1101/2022.05.17.492392
A1 Laura Luebbert
A1 Lior Pachter
YR 2022
UL http://biorxiv.org/content/early/2022/05/27/2022.05.17.492392.abstract
AB Motivation A 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.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 The manual and source code are available at https://github.com/pachterlab/gget.Contact lpachter{at}caltech.eduCompeting Interest StatementThe authors have declared no competing interest.