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.

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 specification

MinION Mk1D IT requirements

Safety and regulatory information

Our MinION Mk1D FAQs are located here.

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

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.

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.

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.

The image below shows a hardware check for a Flongle Flow Cell using the Flongle adapter:

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

A loading bar will be displayed under the flow cell during the check.

The quality of the flow cell will be shown as one of three outcomes:

1. 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).

2. Green tick (MinION Flow Cell): The number of sequencing pores is above warranty.

3. 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.

To run a sequencing experiment, you will need to purify your DNA or RNA sample and prepare a sequencing library. For more information about sample preparation, refer to the Prepare section of our Documentation.

You can access the MinKNOW protocol by following this link.

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.

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

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’.

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.