Set Up Secondary Analysis
NovaSeq X and NovaSeq X Plus Sequencing Systems allow you to perform multiple DRAGEN analyses in a single sequencing run. Before setting up secondary analysis, make sure you have installed the appropriate DRAGEN application on the instrument. For more information on installing DRAGEN applications, refer to Install Applications.
You can create up to 12 analysis application and reference genome combinations with an additional BCL Convert-only application. For each combination, you can use up to 32 configurations using a different library prep kit, index adapter kit, or configuration settings for an analysis application and reference genome combination already used.
The following combinations are included in the 12 configuration limit:
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The same analysis application and application version with a different reference genome |
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The same reference genome with a different application or application version |
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A different application or application version with a different reference genome |
Configure secondary analysis as follows.
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Select an application and provide the following configuration settings for your run: |
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[Optional] Configuration description |
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Reference genome (not applicable for DRAGEN BCL Convert) |
When an Illumina library prep kit is selected, adapter sequences for Read 1 and Read 2 automatically populate and cannot be modified. Override cycles also automatically populate.
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Provide additional analysis settings as needed. The settings available or required vary based on the application, application version, and the configuration settings selected. For more information on DRAGEN secondary analysis, refer to Illumina DRAGEN Bio-IT Platform support page. |
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To enter sample information, use one of the following options: |
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To import sample information, download the CSV template, add your sample information, and import the edited CSV file. |
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Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, add additional sample rows as needed. Sample IDs can contain up to 20 alphanumeric characters, hyphens, and underscores. |
Fixed-layout index plates require entries for well position. Indexes that do not have a fixed layout require entries for i7 and i5 indexes. i5 indexes must be entered in the forward orientation.
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Manually enter sample IDs and corresponding well positions or indexes. If Not Specified is selected for the library prep kit, enter Index 2 (i5) sequences in the forward orientation. |
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Complete the run configuration. |
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To edit the run details later, select Save as draft. |
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To finalize the run details and make the run available for sequencing, select Save as Planned |
