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# Custom Metabarcoding Reference Database

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[![Twitter Follow](https://img.shields.io/twitter/follow/ephe_bev?style=social)](https://twitter.com/ephe_bev)


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Scripts to convert FASTA files into reference database linked to NCBI taxonomy.
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## Introduction

scripts to create our own reference database with our own sequences only and using the NCBI taxonomy



## Workflow

* inputs:
    * FASTA file

0. get raw fasta files of new sequences with species-names
1. Extract sequence name
2. Check sequence name format
3. Check sequences format (iuapc ambiguity, gaps)
4. Correct NCBI-taxonomy species name (this is semi-automatic)
5. Attribute NCBI-taxonomy taxid
6. Extract names with missing taxid
    1. Attribute NCBI-taxonomy taxid of genus
    2. Run obitaxonommy command for unattributed taxid species
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7. Write fasta file of sequences with their taxid and complete genus-species name
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* outputs:
    * formatted FASTA file
    * .ldx new nodes for missing taxid into the taxonomy to link to existing genus/family taxid

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`raw fasta` --> validate --> `valide fasta` `faulty_format fasta` `faulty_taxon fasta`
`faulty_taxon fasta` --> curate (actuellement Laetitia qui fait ce job) --> `curated_taxon csv`
verifier et corriger à la main le tableau `curated_taxon csv`
`raw fasta` `curated_taxon csv` --> validate --> `valide fasta` et mise à jour de la taxonomy


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## Environment

To create environments with required softwares: 

```
conda env create -f envs/obitools_envs.yaml
conda env create -f envs/pylib_cbdr.yaml
```

* Obitools

```
conda activate obitools
```

* Required python libraries to build custom reference database

```
conda activate pylib_cbdr
```