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. The whole reference database can also be downloaded.

Info 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.

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

Note The oradatafolder can be moved to another location but should keep its structure.

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>

Note The oradatafolder can be moved to another location but should keep its structure.

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.