> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-stratamap/dragen-spatial-transcriptome/analysis-inputs/genome.md).
# Genome
A genome is required for all spatial analyses. The input must be a TAR.GZ containing a genome FASTA and annotation GTF.
### Default Genomes
Spatial-specific Mouse and Human genomes are provided in the genome\_bundle:
* /genomes/mm39.tar.gz
* /genomes/hg38.tar.gz
These genomes are available by default for auto-launch and manual launch analysis.
### Custom Genomes
DRAGEN Spatial Transcriptome supports inputting custom genomes as long as a valid genome annotation file (GTF) and genome (FASTA) are provided. There are two options for producing the genome reference:
1. Contact support and provide the genome (FASTA) and genome annotation file (GTF) for the desired custom genome, and support will send back a genome in the correct format.
2. Use the DRAGEN Reference Builder along with a few manual steps. DRAGEN Spatial Transcriptome supports custom genome usage via this method.
Prerequisites:
* A genome FASTA
* A genome annotation file (GTF), gzipped (example: GENTEST.gtf.gz)
* It **cannot** be named genes.gtf.gz
1. Upload your .gtf.gz and .fa files to the Sequence Hub.
1. Navigate to Projects.
2. Create a new project if necessary.
3. Upload the .gtf.gz and .fa files to the project.
2. Navigate to Apps in the Sequence Hub and search for "DRAGEN Reference Builder".
3. Launch the 4.4.4001 version of the App.
4. Populate the fields in the App with the uploaded files and any other required information, and click Launch Application.\
Example:\
5. Once the application has completed, download the .tar.gz by navigating to the project and selecting the completed analysis. Next, click on the files icon > download > Analysis. This will bring up the following pop-up menu with instructions to download using the BaseSpace Sequence Hub Downloader.\
6. Finally, upload the tar.gz to ICA using the ICA UI or the icav2 command-line tool.
* If using the UI, navigate to the project > data > folder you wish to upload the file to, then drag and drop the file into the designated location.\
7. At this point, the .tar.gz is available and may be selected as the genome for manual execution of the DRAGEN Spatial Transcriptome analysis.
### Local Custom Genome
If running DRAGEN Spatial Transcriptome locally, follow the instructions for creating a custom genome, ending on step 5, which will provide the genome to use locally.
### Troubleshooting
* This process does not guarantee the efficacy of the genome for analysis, only correct formatting.
* If the genome is causing a problem in analysis, it will appear in the FastqFlow stage of analysis. Review the nextflow\_issues.log found in the output files tab; it will include the error message.
---
# 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://help.connected.illumina.com/dragen-stratamap/dragen-spatial-transcriptome/analysis-inputs/genome.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.