Welcome!

gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases.

gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

The databases queried by gget are continuously being updated which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary. If you encounter a problem, please upgrade to the latest gget version using pip install --upgrade gget. If the problem persists, please report the issue.

 
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gget info and gget seq are currently unable to fetch information for WormBase and FlyBase IDs (all other IDs are functioning normally). This issue arose due to a bug in Ensembl release 112. We appreciate Ensembl's efforts in addressing this issue and expect a fix soon. Thank you for your patience.

More tutorials

If you use gget in a publication, please cite*:

Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836

Read the article here: https://doi.org/10.1093/bioinformatics/btac836