Option A: From Run Planner

Use this option when you are planning a new sequencing run and want to auto-launch the Baseline Builder at the end of sequencing.

Step-by-Step Instructions

1. Navigate to BaseSpace Sequence Hub (BSSH) and select your desired workgroup. Log in to your domain first if required.

2. Go to the Runs tab, select New Run, then select Run Planning.

   
3. Set the Analysis Location to BaseSpace/Illumina Connected Analytics.

4. Select DRAGEN systematic noise file builder v4.5 from the Application drop-down menu.

5. Select IDT xGen cfDNA and FFPE library prep from the Library Prep Kit drop-down menu and choose the adapter kits you are using. Click next.

   
6. If needed, modify the read lengths.

7. Complete the sample sheet table. See Tip below for a more straightforward experience.

   
8. Upload your Target BED file.

9. The reference genome defaults to hg38 v6. Modify it if the Target BED file reference genome is different.

10. UMI is enabled by default and can be turned off if preferred.

11. The SNV systematic noise file threshold is optimized at 0.02 and set as the default.

12. Click next to create the Sample Sheet.

Tip. Click on Sample ID and select Fill down to enumerate your samples automatically.

IMPORTANT. When using the Run Planner UI, samples for systematic noise baseline building and the experimental (tumor) samples must be processed on different flow cells. If you need both on the same flow cell, run BCL Convert from Run Planner first, then launch the Baseline Builder app separately from the BSSH or ICA application.