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How do I set up the Flongle for flow cell checks and sequencing?

How do I set up the Flongle for flow cell checks and sequencing?

Prior to inserting a Flongle Flow Cell into the Flongle adapter, the following steps should be performed:

  1. Power on the device or computer and launch the MinKNOW software. Check for an available software update, and if available, update to the latest version.

  2. If using a MinION Mk1B, connect the device to the computer using the provided USB cable.

  3. Insert the Flongle adapter, ensuring you exert moderate downwards pressure to fully seat the adapter in the device. Once inserted the Flongle adapter will be recognized in MinKNOW.

  1. Now a Flongle Flow Cell can be inserted into the adapter, with moderate downwards pressure until you hear a click.

The flow cell should sit evenly and flat inside the adapter, to avoid any bubbles forming inside the fluidic compartments.


Flongle Flow Cells can be stored, unopened, at 2-8 °C for four weeks.

Please note that exposure to air or freezing will irreversibly damage the pores.

A flow cell check is recommended before priming and loading a Flongle Flow Cell to ensure sufficient pores are available to use for your experiment.

Steps for performing a flow cell check-in MinKNOW can be found here.

If a flow cell check results in fewer than 50 pores within the four-week warranty period:

  1. Remove the flow cell from the adapter.

  2. Update the MinKNOW software, if not on the latest version.

  3. Reboot the computer or device.

  4. After powering back on, ensure the Flongle adapter has been detected in MinKNOW prior to re-inserting the flow cell.

  5. Perform one more flow cell check. If still below 50 pores, contact the support team within two business days of performing the QC and include the ID listed on the flow cell, the lot number from the pouch, and the QC results.

  6. Please note that a flow cell replacement will need to be validated prior to the use of the flow cell for sequencing, per our terms and conditions.

When preparing a library to load onto a Flongle Flow Cell, ensure you are using the Flongle branch of the protocol for proper procedure.

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