@@ -8,7 +8,7 @@ This method is based on [OBItools](https://pythonhosted.org/OBITools/welcome.htm
## Installation
To build this reference database, you will a local copy of this repository
To build this reference database, you will need a local copy of this repository
* open a shell
* make a folder, name it yourself, I named it workdir
@@ -40,6 +40,15 @@ You will also need to have the following programs installed on your computer.
## Build a reference database
* Overview of the steps
1. Download the sequences¶
2. Download the taxonomy
3. Use [ecoPCR](https://git.metabarcoding.org/obitools/ecopcr/wikis/home)
to simulate an *in silico* PCR
4. Clean the database
* Run the script
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
@@ -57,7 +66,7 @@ In addition, it includes `EMBL` folder which contains all the sequences and `TAX
## 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.
Now, your reference database can 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/reference_database` 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)
