Create a New Run

1.

If creating a run on-instrument, navigate to the Planned tab as follows.

a.

Select the instrument icon to open the global navigation menu.

b.

Select Runs, and then select the Planned tab.

c.

Proceed to step 3.

2.

If creating a run on a networked computer, the Planned tab displays after signing in.

3.

Select Create run.

4.

In the Run name field, enter a name of your preference to identify the current run.

The run name can contain a maximum of 255 alphanumeric characters, spaces, periods, dashes, and underscores.

5.

[Optional] Enter a description for the run.

The run description cannot contain asterisks (*), brackets ([ ]), or commas (,).

6.

Enter the number of cycles performed in each read:

The total number of read cycles and index cycles cannot exceed the number of cycles specified by the reagent kit. The index cycle limit applies to cycles used as an index, not UMI cycles or trimmed reads.

•

Read 1—Enter up to 151 cycles.

•

Index 1—Enter up to 10 cycles. For a PhiX-only run, enter 0 in both index fields.

•

Index 2—Enter up to 10 cycles.

•

Read 2—Enter up to 151 cycles. This value is typically the same as the Read 1 value.

7.

[Optional] Enter your library tube ID.

The library tube ID is on the label of your library tube strip.

8.

Select Next.

9.

Select your analysis application.

10.

[Optional] Enter a description for the configuration.

11.

Select your library prep and index adapter kits.

For information on adding custom library prep and index adapter kits, refer to Import Custom Library Prep and Index Adapter Kits.

12.

If the field is available, select the reference genome.

13.

Select Next to configure secondary analysis and add the sample information.

For more information, refer to Set Up Secondary Analysis.

Before importing, use one of the following options to generate a sample sheet:

•

Navigate to the remote control software. Select the run name, and then select Sample Sheet. Select Save as to save the sample sheet.

•

Plan a sequencing run in Illumina Cloud Run Planning and use local storage. Export the sample sheet after you finish planning the run.

•

Use a sample sheet located in the output folder of a completed sequencing run.

To create a new sequencing run locally using the sample sheet, do as follows.

1.

If creating a run on-instrument, navigate to the Planned tab as follows.

a.

Select the instrument icon to open the global navigation menu.

b.

Select Runs, and then select the Planned tab.

c.

Proceed to step 3.

2.

If creating a run on a networked computer, the Planned tab displays after signing in.

3.

Select Import sample sheet, and then open your sample sheet v2 file.

For information on sample sheet formatting and requirements, refer to the Sample Sheet v2 Resource.

4.

After the sample sheet is validated, select Next to review the imported run details.

During review, the imported run details are editable.

5.

[Optional] Perform any of the following actions:

•

To edit the run settings or configuration settings, select Edit next to the run or configuration.

•

To delete a configuration, select Delete next to the configuration, and then select Yes, delete.

•

To add another analysis configuration to the run, select Add another configuration.

6.

To save the run, select one of the following options.

•

To edit the run details later, select Save as draft.

•

Select Save as planned to finalize the run details and plan for sequencing.