NovaSeq 6000Dx: TSO 500 Auto-launch Analysis in Cloud

This section provides a guided example of the end-to-end user flow for a sequencing run for TruSight Oncology 500 on NovaSeq 6000Dx (RUO mode). The workflow includes automated data streaming to cloud and auto-launch of secondary analysis minimizing manual touchpoints. The tutorial covers:

1. Instrument and BaseSpace configuration

2. Run Set-up, start and monitoring

3. Accessing data in ICA and BaseSpace

Instrument and BaseSpace Configuration

Configure BaseSpace

Follow BaseSpace Setup instructions to configure sequencing run upload to ICA.

Configure BaseSpace connection on NovaSeq 6000Dx

1. On the RUO side of the instrument, select Instrument Settings.

Instrument Settings

3. Select RUO SETTINGS tab to configure BaseSpace connection.

4. Select the box BaseSpace Sequence Hub: (Optional to upload and store run data in cloud server)

5. Select Run Monitoring and Storage (image below) in the hosting location dropdown menu

6. Choose the region where BaseSpace is hosted from the hosting location dropdown menu

Connecting with BaseSpace

8. Specify the domain name. It is only possible to use a private domain. Contact the IT department to add the correct URLs to the firewall allow list. For further information, please refer to Network Connections and Control Computer Firewall.

Specify domain name

Run Set-up, start and monitoring

Plan the Sequencing Run

BaseSpace Run Planning provides an interface for planning a sequencing run.

1. Navigate to BaseSpace and change to your desired workgroup or personal context. This requires you to login to your domain first.

2. Navigate to the "Runs" tab in BaseSpace. Select the "New Run" button and select "Run Planning".

Run Planning on BSSH

Create a run

1. Use the BaseSpace Run Planning tool to create a planned run.

2. Set the Analysis Location to "BaseSpace/Illumina Connected Analytics" to configure for Cloud analysis.

Set up autolaunch via Run Planner

The configuration input forms vary depending on the instrument, secondary analysis pipeline, and other selections (see Sequencer Auto-launch Analyses Compatibility for details). The images below demonstrate screens using a NovaSeq 6000 Dx instrument with DRAGEN TSO500 analysis.

Run Planning - Configuration 1: Configure a run

3. Select "DRAGEN TSO 500 Analysis Software - 2.5.2" or "DRAGEN TruSight Oncology 500 Analysis Software - 2.5.2 (with HRD)" from the Application drop-down menu.

4. Select TruSight Oncology 500 or TruSight Oncology 500 High Throuput From the Library Prep Kit drop-down menu.

5. Click Next to navigate to the next step.

Run Planning - Configuration 2: Input sample names

6. Enter the names of the samples in the run. Alternatively, you can download a sample template by clicking "DOWNLOAD TEMPLATE" as indicated in the image below, then use it to import the sample information.

Run Planning - Configuration 2: Input per sample configuration

7. In the Per Sample Configuration section, add Sample Type, Pair ID, and Sample Feature. For HRD sample, specify "HRD" in the Sample Feature field, otherwise leave it empty.

Run Planning Review

8. Upon completion, export the sequencing run as a SampleSheet.csv file.

Start the Sequencing Run

Follow the instructions for the sequencer to execute the planned sequencing run for cloud analysis. Attach the SampleSheet.csv saved from the previous step.

Adding SampleSheet

Monitor the Sequencing Run

After a sequencing run is started, use BaseSpace to monitor the run through completion. Use the BaseSpace Run Summary view to track the run progress.

Run Monitoring

View Sequencing Run Output

Refer to Sequencer Run Data in ICA for guidance on viewing the sequencing run data in ICA.

View Secondary Analysis Results

When secondary analysis finishes, the results can be viewed in BaseSpace in the corresponding project. The result files can be viewed and downloaded from the Files tab. In addition, the files can be downloaded using BaseSpace Sequence Hub CLI (BaseSpace CLI) tool.