MinION Mk1D user manual
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MinION: Protocol
MinION Mk1D user manual V M1D_9214_v1_revA_06Nov2024
This is an Early Access device.
For Research Use Only
FOR RESEARCH USE ONLY
Contents
Overview
Installation
- 2. What's in the box
- 3. Installing sequencing software
- 4. Setting up the MinION Mk1D
- 5. Setting up the MinION Mk1D for Flongle
- 6. Hardware check
Pre-sequencing checks and sequencing run
Updating the software
- 9. MinKNOW™ updates
- 10. MinKNOW updates for Windows and MacOS
- 11. MinKNOW updates for Linux
- 12. Re-installing MinKNOW
- 13. Firmware updates
Troubleshooting
Descripción general
This is an Early Access device.
For Research Use Only
1. Device information
The MinION™ Mk1D
The MinION Mk1D is the next generation of portable nanopore sequencing devices. It has been designed to be compatible with modern laptops, computers and the iPad Pro (in combination with the MinION Mk1D iPad Accessory when released) via its USB-C connectivity.
Improved thermal dissipation capabilities of the MinION Mk1D significantly enhances sequencing performance, enabling highly accurate real-time sequencing in an even wider range of environments than its predecessor, the MinION Mk1B. The MinION Mk1D also has intuitive status LEDs to enable you to identify the status of the device at a glance.
The MinION Mk1D can be used with MinION Flow Cells or Flongle™ Flow Cells with the use of the Flongle adapter. The MinION Mk1D device can be used for both DNA and RNA sequencing and is operated using the MinKNOW™ software, which controls the device and flow cells, collects the sequencing data, and performs basecalling.
The hardware
Component | Specification |
---|---|
Size (H x W x D) (mm) | 13 x 55 x 125 |
Weight (g) | 130 |
Maximum rated power (W) | 7.5 |
Installation ports | 1 x USB-C |
Software installed | MinION driver |
Sequencing temperature | Designed to sequence at environmental temperatures of +10°C to +35°C* |
Installation requirement | Maintain 5 cm clearance to all but the bottom face of the device. Do not place the device on top of a laptop/computer. |
*Functional range of electronics is within environmental temperatures of +5°C to +40°C
MinION Mk1D information
FAQs
Our MinION Mk1D FAQs are located here.
2. What's in the box
What's in the box
The MinION Mk1D is shipped with:
- 1x MinION Mk1D
- 1x USB-C to USB-C cable (0.5 m)
- 1x Configuration Test Cell (CTC)
- 1x Quick Start Guide
- 1x Safety and regulatory documentation
The components of the MinION Mk1D are shown below:
Lid - Push up and flip open the lid to access the inside of the device and insert a flow cell. Close the lid on top of the flow cell during use.
Clip - The clip pops up when the lid is opened and holds the flow cell/CTC securely in place. When a flow cell/CTC is removed and the lid is fully closed, the clip retracts into the device.
Configuration Test Cell (CTC) - The CTC is a non-functional flow cell that is used during the hardware check to ensure that the communication between the flow cell, device, and computer is working correctly.
USB-C Port - The USB-C port is for connecting the MinION to the host computer for powering the device and data transfer.
Status LEDs - The status LEDs provide information about the status of the device when it is connected to a computer with the MinKNOW software running.
When the device powers on, the LEDs change from yellow to amber to cyan and then to solid white.
- White LED: no flow cell inserted
- Blue LED: flow cell inserted, script completed successfully
- Green (scrolling) LED: script running
- Red (flashing) LED: script finished with error
Note: the LED statuses are fully implemented in the MinKNOW™ 24.06.16 release. Earlier releases will show a constant cyan colour.
3. Installing sequencing software
IT requirements
Please consult the IT requirements document to ensure your computer meets the specification to run the MinION Mk1D. If your computer does not meet the requirements, sequencing performance may be compromised.
Downloading and installing MinKNOW™
All Oxford Nanopore devices use MinKNOW™ as the primary software. The MinKNOW software carries out several core tasks: data acquisition, real-time analysis and feedback, basecalling, data streaming, controlling the device, and ensuring that the platform chemistry is performing correctly to run the samples. MinKNOW takes the raw data and converts it into reads by recognition of the distinctive change in current that occurs when a DNA/RNA strand passes through the nanopore. MinKNOW then basecalls the reads and writes out the data for onward analysis.
Please follow the MinKNOW protocol for information on how to install the latest version of the software on Windows, MacOS or Linux.
IMPORTANTE
MinKNOW™ version
Please ensure MinKNOW version 24.06.16 or later is installed on your device to enable full functionality of the MinION Mk1D. Earlier versions do not support the MinION Mk1D.
4. Setting up the MinION Mk1D
Instrumental
- MinION Mk1D
- Configuration Test Cell
Open the MinKNOW software.
Use the supplied USB-C cable to connect your MinION Mk1D to a USB-C port on your computer.
The MinION will appear in MinKNOW.
IMPORTANTE
Connecting MinION Mk1D to your computer
Only USB-C ports are supported to connect your MinION Mk1D to your computer. USB-A to USB-C adapters or USB-A to USB-C cables are not supported. USB-A ports typically cannot deliver enough power for the MinION Mk1D and may compromise sequencing performance.
Ensure the device has 5 cm clearance to all but the bottom face and is not placed on top of a heat source such as a computer.
Open the lid of the MinION Mk1D.
Insert the Configuration Test Cell (CTC).
(a) Ensure you press down firmly onto the CTC.
(b) Then close the lid over the CTC.
The status LEDs on the MinION Mk1D will now turn from white to blue.
FIN DEL PROCESO
The MinION Mk1D is ready for the hardware check to be performed.
Please refer to the hardware check section in this manual.
If you have problems with your device appearing in MinKNOW, please refer to the FAQ here.
5. Setting up the MinION Mk1D for Flongle
Instrumental
- MinION Mk1D
- Flongle adapter
Place the Flongle adapter into the MinION Mk1D.
The adapter should sit evenly and flat on the MinION Mk1D. This ensures the flow cell assembly is flat during the next stage.
Close the MinION Mk1D lid and connect the MinION Mk1D device to the host computer using the USB-C cable supplied.
FIN DEL PROCESO
The Flongle adapter is ready for the hardware check to be performed.
6. Hardware check
IMPORTANTE
Hardware check
A hardware check should be performed on all new devices or when software has been updated. This uses the Configuration Test Cell (CTC) that comes with the device.
Note: If using a Flongle Flow Cell, we recommend regularly checking the Flongle adapter by inserting the empty adapter and completing a hardware check. For checking the device, use a MinION CTC, even if a Flongle Flow Cell will be used for sequencing.
Select the sequencing device connected to the computer.
Navigate to the start homepage and click 'Hardware check'.
Click 'Start' for the check to begin.
Ensure the position selected is ready to start, as indicated on the GUI.
For MinION Flow Cells:
For Flongle Flow Cells:
Note: To check the hardware, insert the empty Flongle adapter. To check the device or position for the flow cell, insert a MinION CTC.
You will be automatically navigated to the Sequencing Overview page.
The image below shows a hardware check for a Flongle Flow Cell using the Flongle adapter:
FIN DEL PROCESO
The hardware check will complete after approximately one minute.
Hardware check pass is indicated by a green check icon.
A yellow check icon is a fail.
- Flongle hardware check pass
- MinION hardware check pass
- Flongle hardware check fail
If the hardware check fails, remove and reinsert the CTC, and run a hardware check again. If the check fails for a second time, please contact Customer Support (online Live Support).
7. Flow cell check
Flow cell check
It is essential that a flow cell check is performed to assess the number of pores available before loading a DNA or RNA library onto the flow cell.
Oxford Nanopore will replace any unused flow cell that falls below the warranty number of active pores within twelve weeks of purchase for MinION Flow Cells and four weeks for Flongle Flow Cells, provided that you report the results within two days of performing the flow cell check and you have stored the flow cells according to the storage conditions.
Flow cell | Minimum number of active pores covered by warranty |
---|---|
Flongle Flow Cell | 50 |
MinION Flow Cell | 800 |
Navigate to the Start page and select 'Flow cell check' to open the flow cell check page.
When the MinION Flow Cell type and flow cell ID have been recognised, click 'Start' to begin.
Note: For Flongle, ensure to fill in the Flow cell ID.
IMPORTANTE
For Flongle, Flow cell ID is not automatically assigned in MinKNOW. It is imperative the Flow cell ID is entered in the correct format: ABC123 i.e. ([A-Z] x 3 [0-9] x 3).
The ID is case sensitive with no spaces. The MinKNOW software will not allow you to proceed until the Flow cell ID has been entered correctly.
You will be notified in the bottom right corner of the GUI if any information entered is in the wrong format or missing.
The Flongle Flow Cell ID is shown in the blue box below:
You will be automatically navigated to the Sequencing Overview page.
A loading bar will be displayed under the flow cell during the check.
Flow cell health indicators
The quality of the flow cell will be shown as one of three outcomes:
Yellow exclamation mark (Flongle Flow Cell): The number of sequencing pores is below warranty. Take the flow cell out of the device, re-insert it and run a flow cell check again. If the flow cell is still below warranty, contact Customer Support (online Live Support).
Green tick (MinION Flow Cell): The number of sequencing pores is above warranty.
Orange question mark (Flongle Flow Cell): A flow cell check has not been run on the flow cell during this MinKNOW session.
Note: The indicator of quality will only remain visible during a MinKNOW session. Once the MinKNOW session has ended, the status of the flow cell will be erased.
8. Sequencing and monitoring the experiment
For instructions on how to set up a sequencing experiment and how to monitor the progress of the experiment, refer to the MinKNOW protocol on Oxford Nanopore Community.
9. MinKNOW™ updates
IMPORTANTE
MinKNOW updates
Please ensure MinKNOW version 24.06.16 or later is installed on your device to enable full functionality of the MinION Mk1D. Earlier versions do not support the MinION Mk1D.
Full details of MinKNOW updates will be communicated in Oxford Nanopore's Community announcements section. The release note contains information about new features, bug fixes and known issues. We strongly recommend you stay up to date with the latest release to ensure you have access to the latest features and bug fixes.
10. MinKNOW updates for Windows and MacOS
Updates for Windows and MacOS
Availability of updates to the MinKNOW software are indicated via a pop-up when first opening the software in the MinKNOW Host settings section or can be downloaded directly from the downloads page on Oxford Nanopore's Community.
Check for an update.
You can check for updates using one of these options:
Open MinKNOW via the desktop icon. The auto-updater will automatically check for updates when connected to the device. If there is a new update, a pop-up will appear and direct you to the software downloads page.
In MinKNOW, go to 'Software' in the Host settings and click ‘Get Update’. This will direct you to the software downloads page on Oxford Nanopore's Community page.
Navigate directly to software downloads.
When on the software downloads page, navigate to the section titled 'MinKNOW Software for the MinION Mk1B, Mk1D, and the PromethION 2 Solo (P2 Solo) Devices' and download the installer for your device.
When the installer is downloaded, follow instructions on the installer to install it.
Once the install is complete, you should power cycle your device prior to using MinKNOW.
Note: You will not be able to update your device if connected remotely or if a run is in progress.
11. MinKNOW updates for Linux
To update MinKNOW to a new version:
For GPU:
sudo apt clean
sudo apt update
sudo apt install ont-standalone-minknow-gpu-release
For CPU:
sudo apt clean
sudo apt update
sudo apt install ont-standalone-minknow-release
The latest version of MinKNOW will be installed. Once these commands have completed successfully without errors, reboot the device:
sudo reboot
12. Re-installing MinKNOW
IMPORTANTE
Re-installing MinKNOW updates
In some cases (e.g. if there is a problem with the version of MinKNOW that you are using), it may be necessary to re-install the software. To do this, first do a full uninstall of the current version by following the instructions in this Support article: How to uninstall MinKNOW Software for the MinION Mk1B, Mk1D and P2 Solo Devices.
13. Firmware updates
Firmware updates
With some software updates, the firmware installed on the MinION Mk1D may also need updating. The firmware is automatically updated on the MinION Mk1D the first time the device is plugged in after a MinKNOW update that includes new firmware. When the firmware is updating on the MinION Mk1D, the device will not be selectable in MinKNOW and will display a message that it is updating firmware. The LEDs will also indicate the progress of the update before the device is restarted and the LEDs return to the normal state.
Updating the firmware takes approximately 2.5 minutes. During this time, do not unplug the device from the computer.
Firmware updates on earlier software versions prior to 24.11 will not provide feedback in the MinKNOW UI or on the status LEDs while the firmware is being updated. For the 2.5 minutes while the firmware is being updated, the device may not appear in MinKNOW or may show as ‘device disconnected’.
14. Export logs
Location of Export Logs for Troubleshooting
If you are having problems with your MinION Mk1D or the MinKNOW software, log files are often required for Customer Support to diagnose the issue. Log files can be found in:
Windows: C:\Data\logs\
Mac: /var/log/MinKNOW/
Ubuntu: /var/log/minknow/
The Dorado basecalling logs can be found in the following default locations:
Windows: C:\Data\dorado_logs\
Mac: /var/log/dorado/
Ubuntu: /var/log/dorado/
Note: On Windows, if you have set MinKNOW to output to a non-default location, the logs will be in the 'logs' subdirectory in your output folder.