# GTDB Precurate
[](https://pypi.python.org/pypi/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:
```bash
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.
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"description": "# GTDB Precurate\n\n[](https://pypi.python.org/pypi/gtdb_precurate)\n\n`gtdb_precurate` is an internally used tool used that provides automatic pre-curation of GTDB trees.\n\n## Installation\n\ngtdb_precurate is available on PyPI and can be installed with pip:\n\n```bash\npip install gtdb_precurate\n```\n\n## Usage\n\nAfter a successful install, the `gtdb_precurate` command should be available.\n\nThe following positional arguments are required:\n\n* `metadata` - This is the path to the metadata file, it should contain a header as the first line.\n The only requirement is that it has the following columns: `formatted_accession` and `ncbi_wgs_formatted`.\n* `red_dict` - This is the path to the RED dictionary output by PhyloRank.\n* `red_decorated_tree` - This is the path to the scaled RED decorated output by PhyloRank.\n* `out_directory` - This is the path to the directory where the output files will be written.\n\nThe following optional arguments are available:\n\n* `--min-bootstrap` - This is the minimum bootstrap value to consider a node to be supported. Default: 95.0.\n* `--debug` - This enables debug logging. Default: False.\n\n",
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