Download the reference

What is the reference genome?

Reference genomes change the whole time

Where do you find the reference?

Many reference genomes are built-in in the Belgian Galaxy server.
Especially plant genomes are abundantly present because the Galaxy server is maintained by a group working on plants. But also human, mouse and Drosophila are supported.

If the genome you need is not built-in in Galaxy, you have to download it from:

• Ensembl: http://www.ensembl.org/
• UCSC: http://genome.ucsc.edu/
• NCBI: https://www.ncbi.nlm.nih.gov/

The resource that is considered the best choice is Ensembl but it only supports higher eukaryotes.

After download, upload it to your Galaxy history and you’re good to go!

How to download the reference from Ensembl?

Ensembl versus UCSC

Different names for the same genome

Which genome do you use for variant analysis?

For exome sequencing you also need annotation