The **curegen** module produces the curation CSV file taking advantage of geonames and ete3 dependencies. This curation CSV file can be use to perform automatic curation with the command `mkbdr validate --curate`.
# Inputs
* Faulty taxonomy FASTA file (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#faulty-taxonomy-fasta-file))
* (optional) NCBI taxonomy files (see description [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#ncbi-taxonomies-file))
# Command-line Arguments
This table summarizes the command-line arguments which are using by `mkbdr curegen`.
| complete flag argument | short flag | Default value | Summary |
| --- | --- | --- | --- |
| `--fasta` | `-f` | NA | path of the input faulty taxonomy barcodes sequences FASTA file |
| `--output_prefix` | `-o` | NA | prefix of the output curation CSV file such as prefix.csv |
| `--database_globalnames` | `-d` | 'Fishbase Cache' | Name of the selected database from GlobalNames i.e. 'Catalogue of Life' or 'Fishbase Cache' |
| `--ncbi_taxdump` | `-n` | NA | path of NCBI taxonomy folder |
