... | @@ -54,7 +54,7 @@ mkbdr validate --fasta raw.fasta --output_prefix res --curate curation_table.csv |
... | @@ -54,7 +54,7 @@ mkbdr validate --fasta raw.fasta --output_prefix res --curate curation_table.csv |
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`curation_table.csv` is read to perform curation on species name of records in `raw.fasta`.
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`curation_table.csv` is read to perform curation on species name of records in `raw.fasta`.
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### Using a local NCBI taxonomy
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### Using a local NCBI taxonomy:
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* To run mkbdr with your own NCBI taxonomy located at path/to/ncbi_taxo you have to add the argument `--ncbi_taxdump_load` to your command for the first time:
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* To run mkbdr with your own NCBI taxonomy located at path/to/ncbi_taxo you have to add the argument `--ncbi_taxdump_load` to your command for the first time:
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... | @@ -86,7 +86,7 @@ mkbdr validate --fasta raw.fasta \ |
... | @@ -86,7 +86,7 @@ mkbdr validate --fasta raw.fasta \ |
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### Using a local NCBI taxonomy, performs a curation which add new species to your local taxonomy
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### Using a local NCBI taxonomy, performs a curation which add new species to your local taxonomy:
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* To run mkbdr in order to add new species, you have to allow edition of local NCBI taxonomy files with the argument `--ncbi_taxdump_edition`. To specify the location of NCBI taxonomy folder to edit, add the argument `--ncbi_taxdump`. To apply a curation, add the argument `--curate`. Thorough description of curation CSV file is available [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#curation-file).
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* To run mkbdr in order to add new species, you have to allow edition of local NCBI taxonomy files with the argument `--ncbi_taxdump_edition`. To specify the location of NCBI taxonomy folder to edit, add the argument `--ncbi_taxdump`. To apply a curation, add the argument `--curate`. Thorough description of curation CSV file is available [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#curation-file).
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