Create a Run
Use the following steps to set up a run in Illumina Run Manager either on the NovaSeq 6000Dx or using a browser on a networked computer. Sample data can be entered manually or by importing a sample sheet.
1. | From the Runs screen, select Create Run. |
2. | Select the DRAGEN for Illumina DNA Prep with Enrichment Dx app, and then select Next. |
3. | On the Run Settings screen, enter a run name. The run name identifies the run from sequencing through analysis. |
4. | [Optional] Enter a run description to further identify the run. |
5. | Make sure that the Library Prep Kit selected is an Illumina DNA Prep with Enrichment Dx library prep kit. |
6. | Select the desired index adapter kit. |
7. | Enter the Read Length. |
Read 1 and Read 2 have a default value of 151 cycles.
Index 1 and Index 2 have a fixed value of 10 cycles.
8. | [Optional] Enter a library tube ID. |
9. | Select Next. |
Use the table on the Sample Data screen to enter sample information manually. Alternately, select Import Samples to upload sample information. For information on importing sample information, refer to Import Samples.
Enter Samples Manually
1. | Enter a unique sample ID in the Sample ID field. |
2. | Use the Plate - Well Position to select the well position. |
The i7 Index, Index 1, i5 Index, and Index 2 fields populate automatically.
3. | [Optional] Enter a library name. |
4. | Add rows and repeat steps 1–3 as needed until all samples have been added to the table. |
5. | Select Next. |
A template (*.csv) is available for download on the Sample Data screen when planning a run in Illumina Run Manager using a browser on a networked computer.
1. | Select Download Template to download a blank CSV file. |
2. | From the CSV file, enter the sample information and save the file. |
The sample sheet CVS file includes the following data columns: Sample ID, Plate - Well Position, Optional Library Name.
3. | Select Import Samples and browse to the location of the CSV file. |
4. | Select Next. |
1. | Select the desired analysis workflow: |
• | FASTQ generation |
• | Germline FASTQ and VCF generation for a germline workflow |
• | Somatic FASTQ and VCF generation for a somatic workflow |
2. | [Optional] If desired, select the Generate ORA compressed FASTQs checkbox to enable FASTQ ORA compression. |
3. | [VCF generation workflows] Use the Manifest File Selection dropdown menu to select a manifest file. A manifest file is required input for the DRAGEN for Illumina DNA Prep with Enrichment Dx. The manifest is a tab-delimited BED (*.bed) file that specifies the names and locations of targeted reference regions. |
4. | [Somatic FASTQ and VCF generation workflow] Use the Noise File Selection dropdown menu to select a noise file. A BED file with site-specific noise level can be specified for filtering out systematic noise. For more information, refer to Noise Filtering. |
5. | Select Next. |
1. | On the Review screen, review the information entered on the Run Settings, Sample Data, and Analysis Settings screens. |
2. | Select Save. |
The run is saved on the Planned tab on the Runs screen.