Set up a Custom Reference Genome

In order to use a custom reference genome in Local Run Manager, the genome files must be set up with a specific folder structure.

1.

In C:\Illumina\Genomes, create a folder named for the species of your reference genome.

2.

In the species folder, create a folder named for the agency that published the reference genome.

For example, UCSC, NCBI, or Illumina.

3.

In the agency folder, create a folder named for the version of the reference genome.

For example, hg19, mm9, or 2005-10-07.

4.

In the version folder, create a folder named WholeGenomeFasta.

5.

Rename the reference genome FASTA file to genome.fa.

6.

Add genome.fa and its associated GenomeSize.xml file to the WholeGenomeFasta folder.

The path to the reference genome is:

C:\Illumina\Genomes\<Species>\<Agency>\<Version>\<Sequence>\WholeGenomeFasta\genome.fa