- clone the project (see [Installation](#installation) section)
- fulfill [config.sh](config.sh) and read [ecoPCR ](https://pythonhosted.org/OBITools/scripts/ecoPCR.html?highlight=ecopcr) documentation
## Build a reference database
Once you have fulfilled the [config.sh](config.sh) files with the right parameters, simply run the following command into the current folder `reference_database`
```
bash build_bdr.sh
```
It will be very long to download the sequences and process the *in silico* PCR and filtering steps. Be sure you can run without interruption this script for several days.
I recommand you to open [build_bdr.sh](build_bdr.sh) and to run it step by step. For more information, this script is based on the [OBItools](https://pythonhosted.org/OBITools/welcome.html#installing-the-obitools)'s tutorial available [here](https://pythonhosted.org/OBITools/wolves.html).
## Results
let's define {prefix} as the prefix of the names of reference database as it's defined in [config.sh](config.sh)
The folder of the project will contain `{prefix}_*.sdx` files and a `db_{prefix}.fasta` file.
In addition, it includes `EMBL` folder which contains all the sequences
## Use the reference database
Now, your reference database ban be used for taxonomic assignment in our pipeline to generate species environmental presence from raw eDNA data.
You can use the absolute path of the folder of your reference database as the `/path/to/baseofreference` argument in [only_obitools](http://gitlab.mbb.univ-montp2.fr/edna/only_obitools) and [snakemake_only_obitools](http://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools)