GTDB-Tk¶
GTDB-Tk assigns objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. The bundle packages version 2.4.1.
Usage example¶
The following command can be executed in the terminal to load the bundle:
The module makes the gtdbtk and download-db.sh commands available. The
gtdbtk_shell command can be used to access a shell in the bundle.
Run pet list -t gtdbtk for a list of examples.
Performance notes¶
No performance notes available
Recommended resources per session¶
GTDB-Tk should be run on a system with at least 128 GB of RAM and 8 threads. The minimum memory is taken from Resource usage optimization question and minimum threads from GTDB-Tk performance
Benchmarks¶
No benchmarks available.
Community guides and tutorials¶
- No community guides available.
Official site and documentation¶
Licensing information¶
GTDB-Tk is licensed under the GPLv3 license.
Primary citation¶
GTDB-Tk v2: memory friendly classification with the genome taxonomy database Open Access Pierre-Alain Chaumeil , Aaron J Mussig , Philip Hugenholtz , Donovan H Parks Bioinformatics, Volume 38, Issue 23, 1 December 2022, Pages 5315–5316, doi
External guides and resources¶
- If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za