> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002685.md).

# 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 *Local Run Manager* > *Tools* > *System Settings* > *System Configuration*.

![](/files/oDon87v2tK0lgOHQGRym)

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

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 **Sequence**.
5. In the Sequence folder, create a folder named **WholeGenomeFasta**.
6. Rename the reference genome FASTA file to **genome.fa**.
7. Add **genome.fa** and its associated **GenomeSize.xml** file to the **WholeGenomeFasta** folder. Example of the file path for the hg19 UCSC reference genome: **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](https://support.illumina.com/sequencing/sequencing_software/local-run-manager/documentation.html).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2685), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002685%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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