# References Installation

For decompression of FASTQ.ORA derived from specific species/models, the reference that has been used at compression needs to be downloaded from the [ORA Support Site](https://support.illumina.com/sequencing/sequencing_software/DRAGENORA.html). The whole reference database can also be downloaded.

{% hint style="info" %} <mark style="color:blue;">**Info**</mark>\
For the default human reference, there is no need to add this extra step. The default human reference is already included in the DRAGEN ORA Decompression Software.\\
{% endhint %}

## Linux or mac

### Extract a specific reference

**1.** Move the downloaded archive to the `oradata` directory

```
mv yourdownloadpath/<genus_specificname>.tar.gz yourpath/oradata
```

**2.** Navigate to the `oradata` directory

```
cd yourpath/oradata
```

**3.** Extract the archive file using the following command:

```
tar -xzvf <genus_specificname>.tar.gz (Linux)
tar -xzvf <genus_specificname>.tar.gz (Mac)
```

When the extraction of the specific reference is completed on Linux OS, the `orad.2.7.0.linux` folder should be structured as follows with example on gallus\_gallus reference:

orad.2.7.0.linux

   |\_\_\_orad

   |\_\_\_oradata

          |\_\_\_refbin

          |\_\_\_Gallus\_gallus

               |\_\_\_refbin

               |\_\_\_readme\_gallus\_gallus

{% hint style="info" %} <mark style="color:blue;">**Note**</mark>\
The `oradata`folder can be moved to another location but should keep its structure.\\
{% endhint %}

### Extract the full database

**1.** Move the downloaded archive to the `orad.2.7.0.linux` directory

```
mv yourdownloadpath/oradata.tar.gz yourpath/orad.2.7.0.linux
```

**2.** Navigate to the `orad.2.7.0.linux` directory

```
cd yourpath/ orad.2.7.0.linux
```

**3.** Delete existing oradata folder

```
rm -r oradata
```

**4.** Extract the archive file using the following command:

```
tar -xzvf oradata.tar.gz (Linux)
tar -xzvf oradata.tar.gz (Mac)
```

When the extraction of the full database is completed the `orad.2.7.0.linux` folder should be structured as follows:

orad.2.7.0.linux

   |\_\_\_orad

   |\_\_\_oradata

     |\_\_\_Homo\_sapiens

          |\_\_\_refbin

          |\_\_\_readme\_homo\_sapiens

     |\_\_\_Homo\_sapiens\_bisulfite

          |\_\_\_refbin

          |\_\_\_readme\_homo\_sapiens\_bisulfite

     |\_\_\_\<Genus\_specificname>

          |\_\_\_refbin

          |\_\_\_ readme\_\<Genus\_specificname>

{% hint style="info" %} <mark style="color:blue;">**Note**</mark>\
The `oradata`folder can be moved to another location but should keep its structure.\\
{% endhint %}

## Windows

Extract the downloaded archive with a software that can handle gziped tarballs, such as 7-Zip. Right-click on the archive and select **Extract with**.

When a specific reference is downloaded, a folder with name `<Genus_specifcname>` is extracted. This folder contains the corresponding `refbin` and `readme` files. Move this folder in the location where orad and the default human `refbin` file has been extracted during the installation of the DRAGEN ORA Decompression Software procedure.

When the full database is downloaded, a folder with name `oradata` is extracted. This folder contains subfolders for each specific species which contains the corresponding `refbin` and `readme` files. Move this `oradata` folder in the location where orad and the default human `refbin` has been extracted during the installation of the DRAGEN ORA Decompression Software procedure.


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