Set Up a Sequencing Run (Local Run Manager)

Access	Open Local Run Manager
Local	From the control software menu, select Local Run Manager, and then select Open Local Run Manager.
Remote	From the control software menu, select About to obtain the system IP address. From a computer on the same network as the instrument, open Local Run Manager in Chromium. Use the system IP address to connect.

1.

Make sure that the cartridge is thawed and contains the flow cell and diluted library.

2.

Place the cartridge onto the tray so that the access window faces up and the flow cell is inside the instrument. Do not push the cartridge or tray into the instrument.

3.

Select Close Door to retract the cartridge and close the door.

A panel appears on the left side of the screen to show information from the scanned consumables.

Sign In to BaseSpace Sequence Hub

The BaseSpace Sequence Hub screen appears when the system is configured for Run Monitoring or Run Monitoring and Storage.

1.

To disconnect the current run from BaseSpace Sequence Hub, select Skip BaseSpace Sequence Hub Sign In.

Instrument performance data are still sent to Illumina.

2.

To change connectivity for the current run, select a Configuration option:

•

Run Monitoring Only—Send only InterOp files to BaseSpace Sequence Hub to allow remote monitoring.

•

Run Monitoring and Storage—Send run data to BaseSpace Sequence Hub to allow remote monitoring and analysis.

3.

Enter your BaseSpace Sequence Hub credentials, and then select Sign In.

4.

If the Available Workgroups list appears, select a workgroup to upload run data to.

The list appears when you belong to multiple workgroups.

5.

Select Run Setup.

Select a Run

1.

If the Local Run Manager login screen appears:

a.

Enter your user name and password.

b.

Select Log In.

The screen appears when Local Run Manager is configured to require signing in. By default, signing in is not required.

2.

Select a run from the Run Name list, which lists runs saved in Local Run Manager.

•

To view an updated list, select Refresh.

•

To populate an empty list, select Open Local Run Manager and create a run.

Selecting Open Local Run Manager minimizes the control software and opens Local Run Manager in Chromium.

3.

If you left the control software to create a run, return and select the run. Select Refresh to update the list.

4.

[Optional] Select Edit, and then modify run parameters:

a.

To change Read Type, select or .

b.

To change Read Cycle, enter 26–151 cycles for Read 1. Add one cycle to the desired number of cycles.

c.

To change the output folder for the current run, enter the path to the location or select Browse and navigate to it.

d.

Select Save, which updates the run in both the control software and Local Run Manager.

5.

Select Start Run to initiate the pre-run check.

Review Pre-Run Checks

Pre-run checks include an instrument check and a flow check. The flow check pierces the cartridge seals and passes reagent through the flow cell, so consumables cannot be reused after it starts.

1.

Wait about 15 minutes for pre-run checks to complete.

The run starts automatically after successful completion. Unless the system is muted, a chime sound indicates that the run has started.

Opening the door during the pre-run check or the run can cause run failure.

2.

If an error occurs during the instrument check, select Retry to redo the check.

The instrument check precedes the flow check. When a check is in progress, the bar is animated.

3.

If an error recurs, refer to Error Message Resolution to troubleshoot.

Monitor Run Progress

1.

Monitor run progress and metrics as they appear on the Sequencing screen after cycle 26.

Metric	Description
%Q30 Read 1	The percentage of Read 1 base calls with a Q-score ≥ 30.
%Clusters PF	The percentage of clusters that passed quality filters.
%Occupancy	The percentage of flow cell wells containing clusters.
Projected Total Yield	The expected number of bases called for the run.

2.

To monitor file copying and other run processes, select the control software menu, and then select Process Management.

Unload Consumables

1.

When sequencing is complete, select Eject Cartridge.

The software ejects the used cartridge from the instrument.

2.

Remove the cartridge from the tray.

3.

Remove the flow cell from the cartridge.

4.

Dispose of the flow cell, which has electronic components, in accordance with applicable standards for your region.

5.

Dispose of the cartridge, which contains used reagents, in accordance with applicable standards for your region.

A post-run wash is not necessary because fluidics are discarded with the cartridge.

This set of reagents contains potentially hazardous chemicals. Personal injury can occur through inhalation, ingestion, skin contact, and eye contact. Ventilation should be appropriate for handling of hazardous materials in reagents. Wear protective equipment, including eye protection, gloves, and laboratory coat appropriate for risk of exposure. Handle used reagents as chemical waste and discard in accordance with applicable regional, national, and local laws and regulations. For additional environmental, health, and safety information, refer to the SDS at support.illumina.com/sds.html.

6.

Select Close Door to reload the tray and return to the Home screen.

The software automatically reloads the tray and sensors confirm cartridge removal.