gtdb_precurate is an internally used tool used that provides automatic pre-curation of GTDB trees.
gtdb_precurate is available on PyPI and can be installed with pip:
pip install gtdb_precurateAfter a successful install, the gtdb_precurate command should be available.
The following positional arguments are required:
metadata- This is the path to the metadata file, it should contain a header as the first line. The only requirement is that it has the following columns:formatted_accessionandncbi_wgs_formatted.red_dict- This is the path to the RED dictionary output by PhyloRank.red_decorated_tree- This is the path to the scaled RED decorated output by PhyloRank.out_directory- This is the path to the directory where the output files will be written.
The following optional arguments are available:
--min-bootstrap- This is the minimum bootstrap value to consider a node to be supported. Default: 95.0.--debug- This enables debug logging. Default: False.