The MinION Mk1D is the latest generation of compact nanopore sequencing devices from Oxford Nanopore Technologies. Designed to deliver powerful sequencing performance in a small, portable format, the MinION Mk1D connects directly to a computer via USB-C and is controlled using the MinKNOW™ software. MinKNOW manages key functions including flow cell control, data acquisition, real-time basecalling, and system diagnostics.

Compared with the previous generation MinION Mk1B, the MinION Mk1D offers several enhancements:

• Improved thermal control for consistent performance, even during extended runs or in challenging environments

• Intuitive status LEDs that provide real-time feedback on device activity and run status

• Broad compatibility with modern laptops and desktops that meet the system requirements

The MinION Mk1D supports sequencing of both DNA and RNA samples, and is compatible with MinION™ Flow Cells and Flongle™ Flow Cells (via the Flongle adapter).

Whether you are sequencing in the lab, in the field, or at point of care, the MinION Mk1D offers flexibility, without compromising data quality.

*The device electronics are functional within environmental temperatures of +5°C to +40°C.

MinION Mk1D Technical Specification

MinION Mk1D IT requirements

MinION Mk1D FAQs

Safety and regulatory information

The MinION Mk1D is supplied with the following:

• 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 automatically raises when the lid is opened and secures the flow cell or Configuration Test Cell (CTC). It retracts when the lid is fully closed and no flow cell/CTC is inserted.

Configuration Test Cell (CTC) - A non-functional flow cell used during initial set up and subsequent hardware checks to confirm successful communication between the MinION Mk1D, MinKNOW, and the host computer.

USB-C Port - Used to connect the MinION Mk1D to the host computer for power and data transfer. Requires a USB-C port capable of data transfer (USB 2.0 or higher).

Status LEDs - The status LEDs provide visual feedback on the state of the device when connected to a computer running MinKNOW.

During power-on, the LEDs light up sequentially to indicate device start-up. Once start-up is complete, the LED colour reflects the current status:

Note: Full LED functionality is supported in MinKNOW version 24.06.16 and later. Earlier versions may display a constant cyan LED.

Ensure that your computer meets the specifications outlined in the MinION Mk1D IT requirements document. Using a system that does not meet the recommended specifications may lead to reduced performance, slower basecalling, or failed sequencing runs.

All Oxford Nanopore sequencing devices, including the MinION Mk1D, are operated using MinKNOW, the primary control and analysis software.

MinKNOW manages core sequencing tasks, including:

• Device control and flow cell management
• Data acquisition and real-time feedback
• Basecalling and data streaming
• Monitoring platform chemistry during sequencing

The software interprets the changes in current as nucleic acid strands pass through the nanopore, converting these raw signals into basecalled reads for downstream analysis.

To install MinKNOW on Windows, macOS, or Linux, please refer to the MinKNOW installation protocol for device specific instructions.

Before starting, ensure that MinKNOW is up to date, and that your computer meets the MinION Mk1D IT requirements.

Connecting the MinION Mk1D

The hardware check generates a report in HTML format and contains the following information:

• Number of positions that passed/failed the hardware check on the device
• Date and time that the hardware check was completed
• Hardware check ID
• Device ID

Summary shows the overall result for each position following a hardware check.

Connection check detailed results contains information on whether the connection check passed or failed for the selected position with the option to hide passed positions.

Temperature check detailed results contains information on whether the temperature check passed or failed for the selected position with the option to hide passed positions. Note that the temperature check is not included in the hardware check for MinION Mk1D devices.

An example report is shown below:

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.

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.