# Creating custom reference genomes (non human) to use with DRAGEN apps on BaseSpace Sequence Hub

DRAGEN requires reference genomes to be converted into a **hash table** format.

To use a custom reference genome (non-human) with DRAGEN apps in BaseSpace Sequence Hub (BSSH), use the [DRAGEN Reference Builder app](https://basespace.illumina.com/apps/18468450/DRAGEN-Reference-Builder?preferredversion=)(consideration depends on which DRAGEN App(s) versions will be used for analysis) to convert a reference genome in FASTA format to a hash table. User is recommended checking App Description for the requirement of custom hash table.

Once the DRAGEN reference builder app is done, use DRAGEN apps with Custom Genome option.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-f2e744a2ab8328c2740acab0d1565370cbf0739f%2Fimage1.png?alt=media\&token=474947b1-8866-4d9c-8acc-d951af2b0858)

The DRAGEN apps typically provide built-in support for hg19, hg38, GRCh37, and hs37d5. The Reference Builder app is meant for users who need to generate a custom, non-human or non-standard reference.

**DRAGEN reference builder app is different from Reference Builder (Instruments) app where Reference Builder (Instruments) was used for on-instrument or Run Planning set up analysis with custom genomes.**

**Where to download the FASTA/GTF file?**

For custom genomes for RNA analysis, Illumina recommends using GTF files (& genomes) from [Ensembl.](https://useast.ensembl.org/info/data/ftp/index.html/)

Users can also download FASTA file from public databases or from [iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).

**How to upload the fasta/GTF files to BaseSpace?**

To upload FASTA/GTF files to BaseSpace Sequence Hub (BSSH): open a project, select the **File** icon, then select **Upload** > **Files** > **Misc**

**The file extension must be .fasta or .fa, or the apps will not recognize it.**

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #7488), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007488%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |