How to add a Custom Reference Genome in Local Run Manager

Local Run Manager (LRM) allows for use of custom reference genomes for alignment.

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

The path to a reference genome is:

C:\Illumina\Genomes(Species)(Agency)(Version)\Sequence\WholeGenomeFasta\genome.fa

The default location for reference genomes in LRM is C:\Illumina\Genomes, However, the default location can be changed.

To check the default location in LRM: From LRM> Tools> System Settings > System Configuration.

To create the specific folder structure for the custom reference genome:

1. In the species folder, create a folder named for the agency that published the reference genome. For example, UCSC, NCBI, or Illumina.

2. In the agency folder, create a folder named for the version of the reference genome. For example, hg19, mm9, or 2005-10-07.

3. In the version folder, create a folder named Sequence.

4. In the Sequence 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. Example of the file path for reference genome:

   1. C:\Illumina\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta\genome.fa

Notes:

• The genome column must specify the location for the custom reference genome in the sample sheet. Example of the Genome column in sample sheet: Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta

• In the LRM DNA Amplicon analysis module, variant annotation is supported for human genomes only, and not supported for custom genomes.

For more information, see the Local Run Manager software guide.

For any feedback or questions regarding this article (Illumina Knowledge Article #2685), contact Illumina Technical Support [e-mail].