GTDB-Tk

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

Notifications about GTDB-Tk releases will be available through the GTDB Twitter account https://twitter.com/ace_gtdb.

Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the GTDB should be sent to the GTDB team.

Running GTDB-Tk

  1. Install GTDB-Tk (or use the third-party web application) (Installing GTDB-Tk)

  2. Access the help documentation Commands, or view the program help menu: gtdbtk -h

  • Note: Individual help can be accessed via the specific command, e.g.: gtdbtk classify_wf -h

Citing GTDB-Tk

We encourage you to cite GTDB-Tk and the third-party dependencies as described in References.

Running GTDB-Tk