... | ... | @@ -16,7 +16,7 @@ This table summarizes the command-line arguments which are using by `mkbdr valid |
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| `--fasta` | `-f` | NA | path of the input barcodes sequences FASTA file |
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| `--output_prefix` | `-o` | NA | Output files prefix names |
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| `--curate` | `-c` | NA | path of the input taxonomy curation CSV file. Header must be current_name;ncbi_name;genus;family;ncbi_rank. A curation CSV file can be generated with the command curegen |
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| `--curate` | `-c` | NA | path of the input taxonomy curation CSV file. Header must be current_name;ncbi_name;genus;family;ncbi_rank. A curation CSV file can be generated with the command curegen (see the [Curegen section](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen) to learn how to produce a curation file) |
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| `--ncbi_taxdump` | `-n` | NA | path of NCBI taxonomy folder |
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| `--ncbi_taxdump_load` | `-l` | FALSE | load NCBI taxonomy from NCBI taxonomy folder path |
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| `--ncbi_taxdump_edition` | `-e` | FALSE | allow curation to edit NCBI taxonomy files in order to add new taxonomy nodes |
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... | ... | @@ -106,7 +106,7 @@ To perform taxonomic assignment in further analysis you need valid FASTA file an |
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In case the faulty format FASTA file is not empty, you have to correct manually the records in your input FASTA file and run again `mkbdr validate`.
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In case the faulty taxonomy FASTA file is not empty, you have to correct the species name of the records in the input FASTA file and run again `mkbdr validate`. You can correct species name manually or use `mkbdr curegen` to generate a curation CSV file that can be use as input of `mkbdr validate --curate` that will apply curation on your input FASTA file.
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In case the faulty taxonomy FASTA file is not empty, you have to correct the species name of the records in the input FASTA file and run again `mkbdr validate`. You can correct species name manually or use `mkbdr curegen` (see [Curegen Section](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen) for details) to generate a curation CSV file that can be use as input of `mkbdr validate --curate` that will apply curation on your input FASTA file.
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