GTDB Precurate

gtdb_precurate is an internally used tool used that provides automatic pre-curation of GTDB trees.

Installation

gtdb_precurate is available on PyPI and can be installed with pip:

pip install gtdb_precurate

Usage

After 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_accession and ncbi_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.