> 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/dragen-v4.6/getting-started/quickstart/dragen-server.md).

# DRAGEN Server

A DRAGEN Server is FPGA-accelerated hardware installed at your site. Your data stays on your network.

Choose this when data cannot leave your facility.

## Before you start

| You need         | Notes                                                                |
| ---------------- | -------------------------------------------------------------------- |
| A DRAGEN Server  | Ordered through Illumina.                                            |
| Prepaid licenses | Server licensing is a prepaid quota assigned to the specific server. |

Review the [Server Site Prep and Installation Guide](https://support.illumina.com/downloads/illumina-dragen-server-site-prep-guide.html).

## Install and verify

{% stepper %}
{% step %}

## Install the software

Download the installer for your DRAGEN version from the [DRAGEN Software Support Site](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/downloads.html), then install it as root.

DRAGEN 4.3 and later support multiple installed versions side by side. For the full procedure, including single-version and multi-version differences, see [DRAGEN Server Installation and Setup](/dragen/dragen-v4.6/product-guides/dragen-v4.6/getting-started.md#on-premises-installation).
{% endstep %}

{% step %}

## Install licenses

A connected server retrieves its assigned licenses automatically, once per day, so usually no action is needed.

If you need to install a license by hand, use the `dragen_lic` tool. See [DRAGEN Server Licensing](/dragen/dragen-v4.6/reference/licensing/onprem_licensing.md).
{% endstep %}

{% step %}

## Run the self test

Confirm the hardware and licensing work before you trust the server with real data. The self test indexes a reference, maps reads, and checks the output against expected results.

```bash
<INSTALL_PATH>/self_test/self_test.sh
```

It takes about 25 to 30 minutes and ends with `SELF TEST RESULT : PASS`. If it fails on a new server, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#technical-support).
{% endstep %}

{% step %}

## Load a reference genome

A reference must be converted to DRAGEN's binary hash table format before use. See [Prepare a Reference Genome](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-reference-support/prepare-a-reference-genome.md).

Keep the hash table on the fast file system, normally `/staging`.
{% endstep %}

{% step %}

## Run your own data

Point DRAGEN at your reference and your FASTQ files, and send output to fast storage.

```bash
dragen \
  -r /staging/human/reference/<reference_hash_table> \
  -1 /staging/test/data/<sample>.fastq \
  --output-directory /staging/test/output \
  --output-file-prefix <sample> \
  --RGID <read_group_id> \
  --RGSM <sample_name>
```

For the full walkthrough, see [DRAGEN Server Installation and Setup](/dragen/dragen-v4.6/product-guides/dragen-v4.6/getting-started.md#running-your-own-test).
{% endstep %}
{% endstepper %}

## Confirm success

The run exits with code 0 and writes output files to the directory you specified. Check that `<sample>.hard-filtered.vcf.gz` and `<sample>.metrics.json` are present.

## What a run costs

Server licensing is priced per gigabase against the prepaid quota assigned to that server.

See [DRAGEN Server Licensing](/dragen/dragen-v4.6/reference/licensing/onprem_licensing.md) and [DRAGEN Pricing and Licensing](/dragen/dragen-v4.6/reference/licensing.md).

## Next steps

* Use a tested command line for your workflow from [DRAGEN Recipes](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes.md).

For help, see [Troubleshooting](/dragen/dragen-v4.6/reference/troubleshooting.md) and [Support](/dragen/dragen-v4.6/reference/technical-assistance.md).


---

# 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/dragen-v4.6/getting-started/quickstart/dragen-server.md?ask=<question>&goal=<endgoal>
```

`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.