# End-to-End User Flow: DRAGEN Analysis

This tutorial demonstrates major functions of the ICA platform, beginning with setting up a project with instrument run data to prepare to use pipelines, and concluding with viewing pipeline outputs in preparation for eventually ingesting outputs into available modules.

In the following example, we start from an existing ICA project with demultiplexed instrument run data (fastq), use the DRAGEN Germline pipeline, and view output data.

## Set-up

This tutorial assumes you already have an existing project in ICA. To create a new project, please see instructions in the [Projects](https://help.ica.illumina.com/home/h-projects#create-new-project) page.

Additionally, you will need the DRAGEN Demo Bundle linked to your existing ICA project. The DRAGEN Demo Bundle is an an [entitled bundle](https://help.ica.illumina.com/home/h-bundles#access-an-entitled-bundle) provided by Illumina with all standard ICA subscriptions and includes DRAGEN pipelines, references, and demo data.

### Linking an Entitled Bundle

For general steps on creating and linking bundles to your project, see the [Bundles](https://help.ica.illumina.com/home/h-bundles) page. This tutorial explores the DRAGEN Germline Published Pipeline, so we will need to link the DRAGEN Demo Bundle to our existing project.

Steps:

* Go to the **Projects > your\_project > Project settings > Details** page
* Click **Edit**
* Click the **+** button, under Linked bundles
* Select the *DRAGEN Demo Bundle*, followed by **Link**.
* Finally, **save** the change.

{% hint style="info" %}
There may be multiple versions of DRAGEN Demo Bundles. This tutorial details steps for *DRAGEN Demo Bundle 3.9.5.* Steps for other versions after 3.9.5 should be similar.
{% endhint %}

DRAGEN Demo Bundle assets will now be available on the *Data* and *Pipelines* pages.

## Pipelines

After setting up the project in ICA and linking a bundle, we can run various pipelines.

### DRAGEN Germline Published Pipeline

This example demonstrates how to run the DRAGEN Germline Published Pipeline (version 3.9.5) in your ICA project using the demo data from the linked DRAGEN Demo Bundle.

The required pipeline input assets for this tutorial include:

* Under **Projects > your\_project > Data**
  * Illumina DRAGEN Germline Demo Data folder
  * Illumina DRAGEN Enrichment Demo Data folder
  * Illumina References folder
* Under **Projects > your\_project > Flow > Pipelines**
  * DRAGEN Germline

#### Launching the DRAGEN Germline Published Pipeline with Demo Data

From the **Projects > your\_project > Flow > Pipelines** page, select *DRAGEN Germline 3.9.5,* and then click **Start analysis.** Initial set-up details require a *User Reference* (pipeline run name meaningful to the user) and a *Subscription* from the drop-down menu under Pricing.

Running the DRAGEN Germline pipeline uses the following inputs which are to be added in the Input Files section:

<table data-header-hidden><thead><tr><th width="128.25390625"></th><th></th></tr></thead><tbody><tr><td>FASTQ files</td><td>Select the FASTQ files in the <em>Illumina DRAGEN Enrichment Demo Data</em> folder and select <strong>Add</strong>.</td></tr><tr><td>Reference</td><td>Select a reference genome from the <em>Illumina References</em> folder (do not select a methyl-converted reference genome for this tutorial)<br>Use for hg38_altaware_nohla-cnv-anchored.v8.tar for example (suggested, if enabling CNV analysis)</td></tr></tbody></table>

The DRAGEN Germline Settings should match:

<table><thead><tr><th width="295.15234375">Field</th><th width="88.2265625">Value</th><th>Notes</th></tr></thead><tbody><tr><td>Enable germline small variant calling</td><td>true</td><td></td></tr><tr><td>Enable SV (structural variant) calling</td><td>true</td><td>If true, Enable map align output must also be set to true</td></tr><tr><td>Enable repeat genotyping</td><td>true</td><td></td></tr><tr><td>Enable map align</td><td>true</td><td><ul><li>When using FASTQ files as input, as in this example, set this to <strong>true</strong> as default.</li><li>When using BAM files as input, set to <strong>true</strong> to realign reads in input BAMs; set to <strong>false</strong> to keep alignments in input BAM files.</li></ul></td></tr><tr><td>Enable CNV calling</td><td>true</td><td><p>Enabling Copy Number Variant calling requires one of the following:</p><ul><li>Enable CNV self normalization is set to <strong>true</strong></li><li>A panel of normals (PON) is provided in the Input Files</li></ul></td></tr><tr><td>Output format</td><td>CRAM</td><td>Other available options for alignments output are BAM and SAM format.</td></tr><tr><td>Enable CNV self-normalization</td><td>true</td><td>Required if Enable CNV calling is set to <strong>true</strong> <strong>and</strong> no panel of normals (PON) is provided in the Input Files.</td></tr><tr><td>Enable duplicate marking</td><td>true</td><td></td></tr><tr><td>Emit Ref Confidence</td><td>GVCF</td><td><ul><li>Use <strong>GVCF</strong> to enable banded gVCF generation.</li><li>To enable base pair resolution in the gVCF, set to <strong>BP_RESOLUTION</strong></li></ul></td></tr><tr><td>Additional Dragen arguments</td><td>-</td><td>You can provide additional <a href="https://emea.support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform.html">DRAGEN</a> arguments here. Left blank for this example run.</td></tr><tr><td>Sample sex</td><td>-</td><td>You can specify the sex of the sample here if known, we will omit this setting for this example run.</td></tr><tr><td>Enable HLA</td><td>true</td><td></td></tr><tr><td>Enable map align output</td><td>true</td><td>The format for alignment output was selected previously in the <em>Output format</em> setting.</td></tr><tr><td>Resources</td><td>keep default</td><td><ul><li>Storage size: Set to <strong>small</strong></li><li>FPGA Medium Tier: Set to <strong>Standard</strong></li><li>FPGA Medium Resources: Set to <strong>FPGA2 Medium</strong></li></ul></td></tr></tbody></table>

Once all parameters have been set, click **Start analysis**

#### Monitoring analysis run status

You can monitor the status of analysis pipeline runs from the **Projects > your\_project > Flow > Analysis** page. See [Analysis Lifecycle](https://help.ica.illumina.com/project/p-flow/f-analyses#lifecycle) for more details.

Click the refresh button (<img src="https://3193631692-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MWUqIqZhOK_i4HqCUpT%2Fuploads%2Fgit-blob-eb825d0821522d733e4394d1a74bfdfa88bd7186%2Fimage%20(42).png?alt=media" alt="" data-size="line">) in upper right corner of the ICA environment page to update the status.

Click on the run to view more information about it. The various tabs under a given run provide additional context regarding the status of the completed run.

If you encounter a failed run, you can find more information in the **Projects > your\_project > Flow > Analyses > your\_analysis > Details** **tab** and on the **Nextflow execution** **tab**.

Analysis run logs can be found on the **Steps** **tab**. Use the sliders next to Stderr and Stdout for more details. Check the box next to *Show technical steps* to view additional log files.

#### Viewing DRAGEN analysis output

DRAGEN analysis output folders are found on the **Projects > your\_project > Data** page, along with all other data loaded to the project (such as assets from a linked entitled bundle). Output analysis will be grouped into folders, so you can click through the folder structure to explore outputs.

## Related Resources

* [DRAGEN Support Site](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform.html)
* [ICA Pricing](https://help.ica.illumina.com/reference/r-pricing)