Difference between revisions of "GTDBTk"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gtdbtk}} |{{#vardefine:url|https://github.com/Ecogenomics/GtdbTk}} <!--CONFI...") |
|||
| (One intermediate revision by one other user not shown) | |||
| Line 24: | Line 24: | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * {{uc:{{#var:app}}}}_DATA_PATH - reference database | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 15:08, 12 April 2022
Description
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and 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.
Environment Modules
Run module spider gtdbtk to find out what environment modules are available for this application.
System Variables
- HPC_GTDBTK_DIR - installation directory
- HPC_GTDBTK_BIN - executable directory
- GTDBTK_DATA_PATH - reference database
Citation
If you publish research that uses gtdbtk you have to cite it as follows:
https://github.com/Ecogenomics/GtdbTk#references