Running-MKBDR.md

+Here, we produce a valid reference database using **MKBDR** and test it with ecotag.
+
+## Installation
+
+
+See [Installing MKBDR](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Installing-MKBDR) for installation instructions.
+
+## Example data
+
+Download example data with:
+
+```
+curl -LJO https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/raw/master/tests/data/raw.fasta
+```
+
+* `raw.fasta`: a FASTA file of 4 records representative sequence of 4 taxon groups. More details about input files [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#representative-sequences).
+
+
+## 1. First validation
+
+
+The module **[validate](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Validate)** produces a valid records FASTA file and faulty records FASTA file.
+
+```
+mkbdr validate --fasta tests/data/raw.fasta --output_prefix res_raw
+```
+
+This will outputs:
+
+```
+Checking arguments...done.
+Validate records...
+Loading local NCBI taxonomy...done.
+4 processed records.
+On these records, 2 are valid, 0 are faulty format and 2 are faulty taxon.
+```
+
+* `res_raw_faulty_format.fasta` : a FASTA file with faulty format records (empty in this example)
+* `res_raw_faulty_taxon.fasta`: a FASTA file with faulty taxonomy records (2 faulty records in this example)
+* `res_raw_valide.fasta`: a FASTA file with correct records that can be use as reference database for taxonomic assignment (2 valid records in this example)
+
+Read more details about output files [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#output-files).
+
+:seedling: On 4 records, `validate` asserted 2 records with a faulty taxonomy. Faulty taxonomy means that the name of the species is unknown in NCBI taxonomy. So it is impossible to use these records in a reference database. We will need to curate their taxonomy to validate these records.
+
+## 2. Curation 
+
+The module **[curegen](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen)** produces a [curation CSV file](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition)
+
+
 
 
 mkbdr curegen --database_globalnames 'Catalogue of Life' --output_prefix res_raw --fasta res_raw_faulty_taxon.fasta