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The GridION
The GridION is a compact benchtop system offering on-demand sequencing with integrated real-time data processing. Up to five MinION or Flongle Flow Cells can be run individually or concurrently, offering a cost-effective access to long-read, real-time nanopore sequencing. The device is operated by the MinKNOW software, which controls the device, experimental scripts, and performs basecalling.
Below is a quick start guide to set up a new device and to start sequencing your library samples. For further details using this device, please see the GridION User Manual.
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Install the GridION device.
Unpack the device in an appropriate laboratory location and attach all the required cables to the device, including the:
- Ethernet
- HDMI or DisplayPort to monitor
- USB for a keyboard
- USB for a mouse
- C13 cable
Ensure the device is connected to a protective earth mains supply and turn the power source on and press the power button on the device. A blue light will appear in the middle of the button.
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Log into MinKNOW.
Double-click on the MinKNOW icon on your desktop.
Click on Log in with your Nanopore account.
Enter your email address and Nanopore password.
The Connection Manager will open, and your device will be the card in the top left corner.
Click on My device card to access and control it.
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Tutorials
These are available to help you get started and run your experiments as easily as possible.
On opening the MinKNOW software for the first time, the tutorials will navigate you through the graphical user interface (GUI). Click Continue tutorial to follow or click the ⁞ to skip.
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Configure your GridION.
To connect your GridION to a single network, use the user interface. A device can be connected to multiple networks which will require a script to be used. For more information, please see the GridION User Manual.
Validate your IP address to ensure it has been correctly set using a static or DHCP address using the command
ifconfig
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Check the time and date of your device.
Verify the time and data of your device is correct to successfully establish a network connection.
Navigate to Device settings in the host settings.
Check the time and date.
Click Change data and time and set the time using custom date/time.
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Reset the default password.
The device is shipped with a default password
grid
that must be reset.Navigate to Device settings in the host settings.
Click Reset password to open the Change password dialogue box.
Enter the current password, followed by the new password.
Click Reset password to confirm the password change.
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Perform a hardware check.
A hardware check must be perfomed on new devices or after software has been updated.
Open the GridION and slide the CTC under the clip for each position. Gently press down onto the CTC until it clicks into place. To check a Flongle Adapter, insert an empty adapter instead of a CTC.
The LEDs above the flow cell position will be blue when initialising and will turn green when they are ready.
Close the device lid.
Navigate to the Start page and click Hardware check.
Click Select all available positions.
Click Start and the hardware check will complete after approximately 1 minute.
After the hardware check has finished, remove the CTCs and store in dry conditions.
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Perform a flow cell check.
A flow cell check must be carried out before loading a DNA or RNA library to assess the number of pores available.
Open the device and slide your flow cell under the clip. Firmly press down on the flow cell. For Flongle, slide the Flongle Adapter under the clip and insert a Flongle Flow Cell.
Navigate to the Start page and click Flow Cell Check.
MinKNOW will recognise the MinION Flow Cell type and IDs.
Note: For Flongle, fill in the flow cell ID manually.Click Start and the flow cell check will begin.
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Set up a sequencing run.
Prime and load your flow cell with DNA or RNA library by following a library prep protocol and set up a sequencing run, as follows:
Navigate to the Start page and click Start Sequencing.
In the Positions tab, fill in the experiment name, sample ID, and select the flow cell type. Click Continue to kit selection.
Note: For Flongle, fill in the flow cell ID manually.Select the kit and any expansion(s) used to prepare the library. Click Continue to run options.
Specify the sequencing run length and minimum read length or keep the default settings. Click Continue to analysis.
Choose your basecaller model and select any available barcoding and alignment options or keep the default settings. Click Continue to output.
Specify your output data location, format and filtering options or keep the default settings. Click Continue to final review.
Click Start.
For further details, please see the Starting a sequencing run section for your device in the MinKNOW protocol.