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What is GTDB-Tk?
What is 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" (GTDB-Tk's README).
How is GTDB-Tk loaded and invoked?
How is GTDB-Tk loaded and invoked?
GTDB-Tk is available in General/miniconda3/4.8.0 and as an environment module. It is recommended to use the MIniconda module as it offers the most up to date version of GTDB-Tk.
From the Miniconda3 module
From the Miniconda3 module
The Miniconda3-4.8.0 module has the GTDB-Tk package installed to the base environment. Additionally, the ~27 GB of external data has been downloaded and $GTDBTK_DATA_PATH is set by the module on load. The below is an example of using GTDB-Tk on Coeus.
$ module load General/miniconda3/4.8.0
$ echo $GTDBTK_DATA_PATH
/scratch/gtdbtk_data_path/release89/
$ gtdbtk
From the environment module
From the environment module
The below can be used to view all of the installations of GTDB-Tk on a particular system, where this example uses Coeus.
$ module avail |& grep -i gtdb
Biosciences/gtdb-tk/0.1.1
Biosciences/gtdb-tk/0.2.1
Biosciences/gtdb-tk/0.2.2
To start GTDB-Tk, use the below.
$ gtdbtk
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