The MinION Mk1C combines the real-time, rapid, portable sequencing of a MinION Mk1B with a Graphical Processing Unit (GPU) and a high-resolution screen. The device applies the technology of the MinION Mk1B with the basecalling power of the MinIT and the additional features of smartphone, such as a cellular modem and touch screen.

* Functional range of electronics +5°C to +40°C

MinION Mk1C IT requirements

MinION Mk1C technical specification

Safety and regulatory information

Our MinION Mk1C FAQs are located here.

The MinION Mk1C is shipped with:

• Configuration Test Cell (CTC)
• Power adapter
• Plugs compatible with UK, US, EU and Australian sockets
• Quick Start Guide

Touch screen The touch screen allows the user to interact with the MinION Mk1C software directly on the device. LED lights There are five LED lights to the right of the touch screen. All five LEDs illuminate white when the device starts up and then cycle as the system software loads. The cycling indicates that the device is working. When a USB is inserted into the MinION Mk1C, all LEDs illuminate and flash three times before the normal cyclical pattern resumes. Lid The lid can be flipped open to access the flow cell housing. Clip The clip holds the flow cell or Configuration Test Cell securely in place. Configuration Test Cell (CTC) The CTC is used during the hardware check to ensure that the communication between the device and the flow cell is working correctly.

The power requirements for the MinION Mk1C using the AC/DC adapter supplied with the device are detailed below.

Oxford Nanopore Technologies does not supply a portable power supply for this purpose and as such it is not officially supported. If you wish to make use of a portable power supply, then it must be compatible with the below specification.

DC power pack requirements

The onboarding process is available when a MinION Mk1C is first switched on to guide users through setting up a network connection, logging into MinKNOW, enabling remote access and running a hardware check.

There are several options to connect to your MinION Mk1C. These are:

General Options

• If you would like to use the sequencing software (MinKNOW) directly on the MinION Mk1C device: Log into MinKNOW using the device GUI and select the MinION Mk1C device on the Connection Manager.
• If you would like to connect to the MinION Mk1C remotely using a computer: Download MinKNOW software and select the MinKNOW icon shortcut and log into MinKNOW. Select the MinION Mk1C device on the Connection Manager to remotely connect.

Advanced users

• Secure Shell access - see the (Advanced) Connecting by the command-line section of the user manual.

MinION Mk1C sequences and basecalls data via the integrated sequencing device and Oxford Nanopore Technologies basecaller - Dorado - in MinKNOW. POD5, FASTQ and BAM files are output and stored locally on the MinION Mk1C in the Data folder.

This folder and the output files can be accessed through File Manager in MinKNOW. For more information, please see the Data management section of this document.

• If you need to update the hostname of the device, run the following command and replace the <new_hostname> portion with your desired hostname (omitting the angle bracket characters <>):

sudo -S hostnamectl set-hostname <new_hostname>

• Power cycle the device by shutting down with the following command, then press the physical power button to turn the device back on:

sudo shutdown -h now

Both options are supported, however if Ethernet is available, we recommend using Ethernet because the connection will likely be quicker and more reliable.

To connect using Ethernet:

1. Connect a Ethernet cable to the device
2. Navigate to network settings in host settings to confirm connection. IP configuration information will appear when connected.

To connect using Wi-Fi, navigate to network settings and toggle Wi-Fi on. Select a network from the Available Networks panel to connect to the internet.

Select Advanced to open Advanced Wi-Fi Configurations. From here, all available networks can be viewed, connected or removed.

The static IP address can be configured through MinKNOW UI for both WiFI and Ethernet. Below is an example for Ethernet.

1. Click Edit in "IP configuration" to open "Edit the IP address configuration" dialogue box.
2. Select either DHCP or Static tab and click Confirm to save.
3. Once the IP address configuration has changed successfully, click Finish to close the dialogue box.

This can be used to connect to the MinION Mk1C in places where there is no network infrastructure, e.g. in the field. To enable hotspot, select the toggle to ON. When active, the device hotspot name will be displayed.

Hotspot configs can be edited to select a channel if required for congested networks where there may be competition for channels.

1. Navigate to the network settings
2. For hotspot, select the toggle to ON
3. Click 'Configure hotspot'
4. Select channel using the dropdown menu
5. Enter new password
6. Click 'Confirm'

The hotspot should be confirmed as specified in the hotspot configs.

1. Locate the MinION Mk1C ID on the underside label of the device:

2. Click on the MinION Mk1C ID under the Wi-Fi Connections Panel in the Control Panel or the options in the right side of the Task Bar

Login with the Security Key: WarmButterflyWings98

3. Access the MinION Mk1C by the File Explorer: Go to \\mc-XXXXXX (XXXXXX is the MinION Mk1C ID) in the Address Bar. You will be prompted for the network credentials on connecting to the MinION Mk1C through File Explorer.

1. Locate the MinION Mk1C ID on the underside label of the device:

2. Click on the Wi-Fi icon on the right of Menu bar at the top of the screen:

Identify the MC-XXXXXX ID in the Network Name under Network Panel (the final option under the Wi-Fi icon), which is show in the window below (left)‡. Selecting the MinION Mk1C ID and clicking Apply will present the Wi-Fi login pop-up. Use the password credentials shown below.

Login with the Password: WarmButterflyWings98

3. Access the MinION Mk1C by the Network browser: Search for Network using Finder. Click on Server in the tab to lower left of the Search bar.

MC-XXXXXX (XXXXXX is the MinION Mk1C ID) will be displayed as a server option. Click the MC-XXXXXX icon, click Connect as under the Search bar and enter the network credentials.

‡ When connecting to your device by SSH, it can be addressed in three different ways:

1. Using DNS
2. Using mDNS
3. Using its IP address directly

In most organisations, central DNS servers are used. If your device is using a 'static' IP configuration, your IT department will have to create a DNS entry for it manually. If your device is using a dynamic (DHCP) IP configuration, the DNS entry will often be created automatically. To SSH into your device using DNS, set the hostname in your client to the device's hostname, e.g. MC-112345.

If DNS is not provided by your organisation or your broadband router, try using mDNS. When your device is connected to a network, it announces its presence to all other nearby devices such as your laptop or PC. If your laptop or PC is configured to recognise these announcements, you can SSH into your device using mDNS by setting the hostname in your client to the device's hostname followed by ".local", e.g. MC-112345.local.

If the above methods are not successful, use the devices IP address directly. The MinKNOW UI shows the IP addresses for each interface in the Settings - Network page. If your device has LAN and Wi-Fi interfaces, each will have a different IP address. To SSH into your device using its IP address, set the hostname in your client to the IP address, e.g. 10.20.30.41.

1. Locate the MinION Mk1C ID on the underside label of the device:

2. Click on the Wi-Fi icon on the right of Menu bar at the top of the screen.

Identify and click on the MC-XXXXXX ID under the Wi-Fi network options icon (shown above). Enter the Wi-Fi password (shown below) in the pop-up Wi-Fi Network Authentication window:

Login with the Password: WarmButterflyWings98

The following window will be presented when you have connected to the MinION Mk1C Wi-Fi router.

3. Access the MinION Mk1C using the Linux File Browser and enter the server address.

Open the File Browser (this can be found using the Search tool). Select Connect to server on the bottom of the list in the left panel. You will need to enter:

smb://mc-110013

The MinION Mk1C contains 1 TB SSD storage, which provides an average capacity of roughly 50 Gbases, stored in .POD5, .fast5 and/or FASTQ format. Once the SSD fills up, you will need to move your sequencing data off the device to a networked storage location. Network drives for data storage can be mounted from either the Device Settings or the File Manager in the Network tab:

• Device Settings:

• File manager:

The MinION Mk1C has two interfaces that we support for data transfer. These are:

• Ethernet port - direct to interface or LAN
• Wi-Fi - direct to interface

Networking with MinION Mk1C. Blue lines indicate a connection via the internet. The black line indicates a wired connection. The computer on the LAN (B.) can be used to configure the device using parameters that are not available through the Admin interface. You can also configure the MinION Mk1C using the Wi-Fi connected device (A.), however network compatibility issues may inhibit the update.

Internet connection:

This configuration requires an ethernet connection to the Local Area Network (LAN) from the MinION Mk1C. The LAN is connected to the internet, which enables updating of MinKNOW on the device.

Interface connection:

An interface, such as a laptop/mobile device/computer, can be wirelessly connected to the MinION Mk1C. Alternatively, the MinION Mk1C may be accessed and controlled by a computer on the LAN.

Other configurations are also possible, however they are not supported by Oxford Nanopore Technologies:

• Ethernet-desktop/laptop computer to control the MinION Mk1C - no internet
• MinION Mk1C Wi-Fi (Client) to a router and desktop/laptop Wi-Fi to a router, which is itself connected to the internet
• It is possible to adapt other data connections through the USB 2.0 port, however, Oxford Nanopore Technologies cannot advise or support this use.

Connecting by the command line via SSH or the terminal enables several options:

• Access and transfer data on to a mounted USB-hard drive - for instructions, see the Data transfer via SFTP section of this user manual.
• Change the output directory from /data
• Change between static and DHCP (dynamic) IP address of the ports on the MinION Mk1C
• Access to the logs

If SSH is enabled in your Windows build, you can use the built-in Windows Command Prompt (CMD). Open a CMD prompt, then enter ssh minit@hostname (e.g. ssh minit@mc-111414):

If it is your first time connecting, you will be asked to confirm the authenticity of the host. Enter yes to continue:

Enter the password to establish an SSH connection. The default password is minit. Please note that characters will not appear on-screen as you type in the password.

If the SSH connection is successfully established, the shell prompt will now read minit@hostname:~$

A third-party SSH client such as Bitvise (example images shown below) or Putty may be used. The following default options can be entered:

Host – device ID or IP address (e.g. MC-111414) Port – 22 Username – minit Initial method – password Password – minit

If a connection is successfully established, Bitvise will automatically open a terminal window and an SFTP browser. Alternatively, you can click on New terminal console or New SFTP window on the left-hand side:

Open a Terminal, then type ssh minit@hostname (e.g. ssh minit@mc-111414):

If it is your first time connecting, you will be asked to confirm the authenticity of the host. Enter yes to continue:

Enter the password to establish an SSH connection. The default password is minit. Please note that characters will not appear on-screen as you type in the password.

If the SSH connection is successfully established, the shell prompt will now read minit@hostname:~$

The LAN interface on the MinION Mk1C can operate in either DHCP (dynamic) mode or static mode. When in DHCP mode, the settings are acquired from the network’s DHCP server. Some networks do not have a DHCP server or you may wish to override the settings it provides. In such circumstances, the static mode can be used.

The static mode comes pre-configured with the following settings:

IP Address/Subnet Mask: 192.168.0.1/24
Default Gateway: 192.168.0.1
DNS Servers: 9.9.9.9, 8.8.8.8

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

We strongly recommend performing a flow cell check before loading a DNA or RNA library to assess the number of pores available.

Oxford Nanopore Technologies will replace any flow cell that falls below the warranty number of active pores within 12 weeks of purchase, provided that you report the results within two days of performing the flow cell check and you have followed the storage recommendations.

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 the 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 support@nanoporetech.com

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

3. Question mark (PromethION 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 your DNA or RNA sample purified and a sequencing library prepared. For more information about sample preparation, refer to the Prepare section of our Documentation.

You can access the MinKNOW protocol by following this link.

Data can be managed and transferred from the file manager tab on the host settings.

Navigate through the tabs to view the data stored:

• Internal tab: Data stored on the connected sequencing device (MinION Mk1C, GridION, PromethION)
• Removable tab: Data stored on a connected removable storage device e.g. USB drive
• Network tab: Data stored on a connected network drive. The network drive must be mounted prior.

Click the icon in the bottom right corner to open Create New Directory and type in a directory name. Click Create.

Navigate to Device settings to view availabe disk space on the device.

Any peripherals plugged in, including USB, can be ejected using the Eject option.

A network drive can also be connected to the device by selecting Mount Network Drive and filing in the required credentials for connecting using a Samba (SMB) server or a Network File System (NFS).

Compatible disk formats: SD and USB on MinION Mk1C supports DOS FAT, Windows 95 FAT, exFAT, and Linux ext(2|3|4).

Please refer to the 'Mount Network Drive' section of this protocol for more information.

For instructions, see the (Advanced) connecting by the command-line section of this user manual.

You can use software like Filezilla, which enables data transfer for mounted hard drives on Linux, Windows, and macOS. It may also transfer using the SFTP protocol which is available whenever an SSH connection can be established.

Filezilla can be downloaded for various OS to enable data transfer from your MinION Mk1C.

The following default options can be entered: Host – device ID or IP address (e.g. MC-111414) Username – minit Password – minit Port – 22

If it is your first time connecting, you will be asked to confirm the authenticity of the host. Check the box to Always trust this host, add this key to the cache and click OK to continue:

If the SFTP connection is successfully established, you will see the Mk1C file directory shown on the right-hand side of the UI. Please note that Filezilla defaults to the home directory (/home/minit):

You can navigate to the /data directory by entering /data into the Remote site field and clicking Enter:

MinKNOW is the software used on nanopore sequencing devices. The software is described in more detail in the MinKNOW Technical Document. The MinKNOW Protocol provides instructions on how to use the software.

The Oxford Nanopore Technologies software will require access to the AWS IP ranges currently listed here:

http://docs.aws.amazon.com/general/latest/gr/aws-ip-ranges.html

Access to the following IP addresses is also needed:

              178.79.175.200  
               96.126.99.215  

Always refer to the release notes for any version-specific commands that may be supplied.

If you meet the requirements below, you can update your device before the microSD card arrives.

Note: there is no guarantee this process will work, as not all vendors of microSD cards have been tested internally at Oxford Nanopore.

All sequencing data stored in the /data folder is retained after the OS upgrade. However, please note that you may need to configure some device settings after the update.

If you use a mounted external storage to the Mk1C, you will need to remount the external storage. Follow the instructions in the Mount network drive section in this user manual.

If you cannot connect to the internet (you may see the error "Unknown connection 'static'"), follow the instructions in the (Advanced) Network configuration - static vs dynamic IP section in this user manual.