# NovaSeq X Run Planning - DRAGEN Germline

BaseSpace Sequence Hub (BSSH) Run Planning is used to generate a valid sample sheet in v2 format compatible for use on NovaSeq X Sequencing Systems. Filling out the run planning input form will produce a sample sheet with the required fields filled in that can be used to auto-launch the DRAGEN Germline Analysis for use with the Illumina TruPath Genome workflow. Refer to [Cloud Analysis Auto-launch](https://help.connected.illumina.com/analysis/analysis_autolaunch) for more information about the Run Planning/ Autolaunch.

For information on the supported variant callers in the Run Analysis settings, refer to the [Cloud Analysis Settings](https://help.connected.illumina.com/illumina-trupath-genome/run-analysis-setup/cloud-analysis-settings) section.

To navigate to Run Planning, open BaseSpace Sequence Hub and navigate to the **Runs** page by using the navigation bar or by opening the menu on the left-hand side. From the **New Run** dropdown menu select **Run Planning**.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-0e356624d2b23d1665c6e4806f4f53736dcd11d2%2Fimage.png?alt=media" alt=""><figcaption></figcaption></figure>

1. Access the appropriate workgroup to plan the sequencing run
2. Select "Runs" from the top panel
3. Select "New Run"
4. Select "Run Planning" from the right-hand dropdown

### Step 1: Specify Run Settings <a href="#specify-run-settings" id="specify-run-settings"></a>

The run settings specifications are described below.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-30719fa0797df8d38a1f6a9fb7a82f932be8b961%2Fimage.png?alt=media" alt=""><figcaption></figcaption></figure>

#### Descriptions

<table><thead><tr><th width="287">Parameter Name</th><th>Required?</th><th>Description</th></tr></thead><tbody><tr><td>Run Name</td><td>Required</td><td>Run Name can contain 255 alphanumeric characters, dashes, underscores, periods, and spaces; and must start with an alphanumeric character, a dash or an underscore.</td></tr><tr><td>Run Description</td><td>Optional</td><td>Run Description can contain 8192 characters except square brackets, asterisks, and commas.</td></tr><tr><td>Instrument Platform</td><td>Required</td><td>Select "NovaSeq X Series" from the dropdown.</td></tr><tr><td>Secondary Analysis</td><td>Required</td><td>Select "BaseSpace / Illumina Connected Analytics" from the dropdown.</td></tr><tr><td>Read 1</td><td>Required</td><td>151 for DRAGEN Germline analysis.</td></tr><tr><td>Index 1</td><td>Required</td><td>Set to "0"<br>Indexing is not supported.</td></tr><tr><td>Index 2</td><td>Required</td><td>Set to "0"<br>Indexing is not supported.</td></tr><tr><td>Read 2</td><td>Required</td><td>151 for DRAGEN Germline Analysis.</td></tr><tr><td>Sample Container ID</td><td>Optional</td><td>Unique identifier for the container that holds the sample.</td></tr></tbody></table>

### Step 2: Specify Configurations

{% hint style="info" %}
On NovaSeq X Series, this page is called "Configuration 1". The top right-hand corner of the UI displays the Read 1, Read 2, Index 1 and Index 2 entered on the previous run settings screen.
{% endhint %}

The run configuration settings specify the analysis options for the run, as shown below.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-3ad18fe38392e7404116b973b728ca3214b375c2%2Fimage%20(77).png?alt=media" alt=""><figcaption></figcaption></figure>

#### Descriptions

<table><thead><tr><th width="287">Parameter Name</th><th>Required?</th><th>Description</th></tr></thead><tbody><tr><td>Application</td><td>Required</td><td>Select "DRAGEN Germline - 4.5.2" for compatibility with Illumina TruPath Genome. Note that a message will appear to use the Illumina TruPath Genome kit and flow cell with this application version.</td></tr><tr><td>Description</td><td>Optional</td><td>Optional Text Field</td></tr><tr><td>Library Prep Kit</td><td>Required</td><td>Select "Illumina TruPath Genome Prep (C2, 2 Samples" or "Illumina TruPath Genome Prep (C8, 8 Samples)" from the dropdown.</td></tr><tr><td>Index Adapter Kit</td><td>Required</td><td>Select "Not Applicable" as indexing is not supported.</td></tr><tr><td>Reference Genome</td><td>Required</td><td>Select "Homo sapiens [1000 Genomes] hg38 v6" from the dropdown. Note that TruPath is only compatible with Hg38 reference.</td></tr><tr><td>Read 1</td><td>Required</td><td>151 for DRAGEN Germline Analysis.</td></tr><tr><td>Index 1</td><td>Required</td><td>Set to "0"<br>Indexing is not supported.</td></tr><tr><td>Index 2</td><td>Required</td><td>Set to "0"<br>Indexing is not supported.</td></tr><tr><td>Read 2</td><td>Required</td><td>151 for DRAGEN Germline Analysis.</td></tr><tr><td>Sample Container ID</td><td>Optional</td><td>Unique identifier for the container that holds the sample.</td></tr></tbody></table>

### Step 3: Specify Run Configuration and Analysis Settings

The run configuration settings specify the analysis settings required for enabling proximity mode in DRAGEN Germline for use with the Illumina TruPath Genome workflow.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-fb88e77dfbff428bc07f34f7fc6a709ce65312e6%2Fimage%20(76).png?alt=media" alt=""><figcaption></figcaption></figure>

#### Descriptions

<table><thead><tr><th width="287">Parameter Name</th><th>Required?</th><th width="231">Description</th></tr></thead><tbody><tr><td>Description</td><td>Optional</td><td>Optional Text Field</td></tr><tr><td>Library Prep Kit</td><td>Required</td><td>Auto-populated from previous step</td></tr><tr><td>Index Adapter Kit</td><td>Required</td><td>Auto-populated from previous step</td></tr><tr><td>Reference Genome</td><td>Required</td><td>Auto-populated from previous step</td></tr><tr><td>Variant Callers</td><td>Required</td><td>Select "None" for running Mapping/Align only.<br><br>Select "Small" for a subset of Variant Callers.<br><br>Select "All" for running all Variant Callers.<br><br>For more information on the supported callers for Autolaunch, <a href="../../run-analysis-setup/cloud-analysis-settings#bssh-run-planning-autolaunch-settings">refer to this section</a>.</td></tr><tr><td>QC Coverage Regions 1</td><td>Optional</td><td>File in BED format used to generate a QC coverage region report</td></tr><tr><td>QC Coverage Regions 2</td><td>Optional</td><td>File in BED format used to generate a QC coverage region report</td></tr><tr><td>QC Coverage Regions 3</td><td>Optional</td><td>File in BED format used to generate a QC coverage region report</td></tr><tr><td>QC Cross Contamination Variants</td><td>Optional</td><td>QC file in VCF file format</td></tr><tr><td>Adapter Read 1</td><td>Required</td><td>Pre-populated with default setting</td></tr><tr><td>Adapter Read 2</td><td>Required</td><td>Pre-populated with default setting</td></tr><tr><td>Sample Table</td><td>Required</td><td><p>Lanes and Sample ID should be filled out based on how the sample will be prepared. Please refer to the Illumina TruPath Genome Assay Guide for additional information.<br><br>The optional Project field is used to specify the associated BaseSpace Project to output data to. If left empty, Project will default to the Project name derived from the Experiment/Run name.<br><br><strong>Note: Only one sample per lane is allowed.</strong> Up to two samples may be specified using the C2 flow cell, while up to eight samples may be specified using the C8 flow cell.</p><p><br><strong>Note:</strong> <strong>Sample IDs must be unique for each Sample.</strong> If the sample is repeated in another run, select a new name. BSSH will combine sequencing data from samples with the same sample ID.</p></td></tr><tr><td><strong>Map / Align Output Format</strong></td><td>Required</td><td>Select "BAM"</td></tr><tr><td><strong>Enable Proximity Analysis</strong></td><td>Required</td><td>Select <strong>"Yes"</strong><br><br>New analysis setting which enables the proximity analysis workflow in DRAGEN Germline. <mark style="color:red;"><strong>Required for use with Illumina TruPath Genome workflow.</strong></mark></td></tr><tr><td><strong>Enable Proximity Visualization</strong></td><td>Optional</td><td>Optional setting used for outputting *.hic files for visualization. Additional run time and compute may be incurred. Refer to Visualizations section here: <a href="broken-reference">Visualize in HiGlass</a></td></tr></tbody></table>

#### Step 4: Specify Run Configuration and Analysis Settings

Once all details are captured and pass validation, review the run information and choose the **Edit** option to correct any information.

For NovaSeq X Sequencing Systems, the run can be saved as a draft or as a planned run (via **Save as Draft** and **Save as Planned** buttons respectively). Once a run is saved as Planned, it will appear on the NovaSeq X Series instrument where it can be selected for sequencing.

For more information about the auto-launch, refer to [Cloud Analysis Auto-launch](https://help.connected.illumina.com/analysis/analysis_autolaunch). For additional information on run planning, refer to [Plan Runs on Basespace Sequence Hub](https://help.connected.illumina.com/basespace-sequence-hub/sequence/plan-runs).


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