Commit effb09dc authored by peguerin's avatar peguerin
Browse files

readme update

parent b299bdde
......@@ -14,6 +14,25 @@ Scripts to convert FASTA files into reference database with NCBI taxonomy.
## Method
1. [Installation](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Installing-MKBDR)
2. Input Files
* [species representative records FASTA file](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#representative-sequences)
* [NCBI taxonomy files]https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#ncbi-taxonomies-file)
* [Curation table file](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#curation-file)
3. [Quick start]()
4. Running MKBDR
* [Module validate - Check taxonomy and format validity](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Validate)
* [Module cureGen - Curation Generation](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Curegen)
* [Module init_ncbi_taxdump - Download NCBI taxonomy](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/init_ncbi_taxdump)
* [Apply taxonomy curation](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Validate#basic-curation)
* [Add new species to NCBI taxonomy](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Validate#using-a-local-ncbi-taxonomy-performs-a-curation-which-add-new-species-to-your-local-taxonomy)
4. [Output results](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/Files-definition#output-files)
5. [How-to guide]()
6. [Reference](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/wikis/home#credits)
7. [Metabarcoding context - discussion to go further]()
## Workflow
![mkbdr](docs/mkbdr.png)
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