> 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/dragen/software-dragen-troubleshooting-list/000007488.md).
# 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.
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.**
\
\
\
| |
| :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *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)*.* |
---
# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.
## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:
```
GET https://knowledge.illumina.com/software/dragen/software-dragen-troubleshooting-list/000007488.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.