> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/illumina-trupath-genome/run-analysis-setup/ica-analysis.md).

# Platform Core Analysis

This section describes the steps required to execute the DRAGEN Germline for TruPath analysis via Illumina BioInsight Platform Core (previously ICA).

### Link Bundles

1. Link the latest DRAGEN bundle (DRAGEN 4.5 shown below) in Platform Core to your project of interest.
2. See Platform Core reference pages for more details on [adding bundles](https://help.ica.illumina.com/home/h-bundles).
3. See Platform Core reference pages for more details on [uploading data](https://help.ica.illumina.com/project/p-data).

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-ea1993b0ea76a3e79b7244ca187e1361346dcb27%2Ftest4.png?alt=media" alt=""><figcaption></figcaption></figure>

### Executing DRAGEN Germline Analysis

**WARNING**: Deviation from these instructions (including adding additional options) may cause pipeline failure.

1. Select the DRAGEN\_Germline\_Whole\_Genome Pipeline and the version of interest. Select to start analysis with that pipeline.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-d82165c3e3923ef174a745b810a2eea72d7750ac%2Fimage%20(85).png?alt=media" alt=""><figcaption></figcaption></figure>

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-7dda53ced49eba0f3923a2ea2021968bc3077362%2Fimage%20(87).png?alt=media" alt=""><figcaption></figcaption></figure>

2. Enter the necessary run information such as user reference tags, outputs and logs folder.\
   Select the necessary input files for the run, including sample inputs. .FASTQ.GZ or .FASTQ.ORA are supported inputs, optionally with an FASTQ list file. Select "Homo sapiens \[1000 Genomes] hg38 v6 Pangenome" for the reference genome.<br>

   <figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-4f55028ae0b4ea22b056b67cc1e3239dfac643d1%2Fimage.png?alt=media" alt=""><figcaption></figcaption></figure>
3. By **default**, Map/Align Options, Variant Calling Options, CNV Options, and SV Options **are enabled** for the pipeline and are recommended. If no Small Variant Calling, CNV or SV Calling is desired, set those options to "False" (screenshot displays the button to click; the box will disappear upon selecting "False" for those settings).

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-fcc23e1acc73f5af03e3a1c39a0f7362c4bb7b01%2Fimage.png?alt=media" alt=""><figcaption></figcaption></figure>

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-d13e8f66e058eff0ab1fef061cc1160731f223d6%2Fimage%20(3).png?alt=media" alt=""><figcaption></figcaption></figure>

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-b68df14a2092d18cb2777e5439a98dd0e48132ee%2Fimage.png?alt=media" alt=""><figcaption></figcaption></figure>

**NOTE**: SV results are turned on to improve CNV calling accuracy, but these results are not verified or supported.

<figure><img src="https://help.connected.illumina.com/~gitbook/image?url=https%3A%2F%2F707781091-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252FL2tTN7buOERM9NKPYYlg%252Fuploads%252Fgit-blob-9b2b0d43d5dd26cd0fd2001293c72f819ca3a1a4%252Fimage%2520%281%29%2520%282%29%2520%281%29.png%3Falt%3Dmedia&#x26;width=768&#x26;dpr=4&#x26;quality=100&#x26;sign=f5cc1556&#x26;sv=2" alt=""><figcaption></figcaption></figure>

4. Navigate to the **Illumina TruPath Genome Options** section of the analysis input settings.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-852522c4100cb0bd891a26b521aa5ceab00a3c1f%2Fimage%20(96).png?alt=media" alt=""><figcaption></figcaption></figure>

5. By **default**, "Enable Proximity Mode" for use with Illumina TruPath Genome is check-marked and enabled. <mark style="color:red;">**NOTE:**</mark> This option must be enabled in order to analyze TruPath data.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-78d6e88f6ff27656785f83f8be812eeace4da6c6%2Fimage%20(79).png?alt=media" alt=""><figcaption></figcaption></figure>

6. (Optional): To output an additional Hi-C output file for visualization, checkmark the option for "Enable Illumina TruPath Visualization"

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-68b35cf3fe14b29e94090eb2bfe38096994a9220%2Fimage.png?alt=media" alt=""><figcaption></figcaption></figure>

7. (Optional): To turn on Multi-Region Joint Detection (MRJD) Calling, checkmark the option for "Enable running Illumina TruPath MRJD." Please refer to the DRAGEN User Guide for more information on Multi-Region Joint Detection.<br>

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-82625ce0344cb6693e08d3d77951cd4cef031efc%2Fimage%20(81).png?alt=media" alt=""><figcaption></figcaption></figure>

8. Confirm configured settings. Start the analysis upon configuring all analysis settings.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-f056e110e35714993e8e4857494c2072a66a64ab%2Fimage%20(94).png?alt=media" alt=""><figcaption></figcaption></figure>

### Visualizations in Platform Core

Upon successful completion of the DRAGEN Germline pipeline with Illumina TruPath Genome enabled, a separate tab called "Genome Viewer" will appear in the analysis landing page.\
Navigate to [Visualize Data in Genome Viewer](/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-platform-core.md) after analysis completes.


---

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