MinIT™ (MinION Mk1B IT) is the IT solution to running a MinION™ without the requirement for any additional processing power or software.

Stand-alone MinIT. The MinIT is a small-footprint IT solution to your sequencing requirements when running a MinION Mk1B.

The MinIT, MinION Mk1B and peripheral screen. The basic set-up of the MinIT, MinION Mk1B and peripheral screen can used to co-ordinate a sequencing experiment.

The MinIT can self-sufficiently manage all the processing needs that the MinION Mk1B's basecaller needs to basecall an entire assay's sequence output, in real-time, over the lifetime of the experiment.

The MinIT contains various IT data trafficking capabilities, such as:

• 2.4 GHz and 5 GHz wireless radios - for connection to the internet and as an option to connect to your wireless-enabled device
• Ethernet (RJ45) port - this enables a wired link to a router for internet or network connection
• USB 3.0 and USB 2.0 ports - these enable connection of the MinION Mk1B and a Solid-State Device (SSD) for data storage

The onboard 8 GB RAM facilitates large file and data manipulation, which is appreciable when a single 72 hour sequencing experiment can generate 100 GB of .fast5 and FASTQ files.

The MinIT contains an onboard SSD of 512 GB, and this is suitable for storage of the .fast5 and FASTQ files, before off-loading to a long-term storage solution.

Along with optimised hardware, the software required for all stages of a sequencing assay comes uploaded and installed on the MinIT.

These include:

• MinKNOW - Graphical User-Interface (GUI), Core utilities and Guppy (basecaller)
• Bream - Protocol loader

For more information on the software on MinIT, see the MinIT, MinKNOW and Data Analysis technical documents.

To connect to the device, download the software 'MinKNOW Stand Alone GUI' for your operating system on the Software Downloads page.

EPI2ME is a product of Metrichor Ltd, a wholly-owned subsidiary of Oxford Nanopore Technologies. EPI2ME provides bioinformatic analysis services that allow the user to take basecalled data and discern biologically relevant information using bioinformatics.

For more information on EPI2ME, please see the EPI2ME Technical Document

A local software version of EPI2ME comes installed on MinIT and, provided that there is a internet connection - (see Hardware introduction) - basecalled data can be analysed in real-time in the cloud. A special configuration of the MinIT is required to co-ordinate real-time analysis; for this the an Ethernet cable (Cat5 or above) should be inserted into the MinIT and wired into a router or network to provide internet access. The wireless (Wi-Fi) radio of the peripheral screen should be used to link the MinIT through a Wi-Fi connection (through its ID on the underside of the MinIT - as cited later in this document). This ensures the MinION can be configured through the peripheral screen, using the MinKNOW GUI and the internet can be accessed through the wired ethernet connection to the cloud.

In order to run MinIT, the user requires a power source of 14–17 VDC, 2 A max current output, which can be delivered from an AC/DC adapter (provided) or a DC battery pack (not provided).

The AC/DC adapter can be powered from 100–260 VAC, 13 A, 50–60 Hz; this constitutes the AC mains supply from various international standard power sources, so that the MinIT can operate globally.

The DC battery provides freedom to sequence with a MinION Mk1B, isolated from an AC mains power supply. Oxford Nanopore Technologies do not recommend any specific model or manufacturer of DC battery pack. Nevertheless, provided that the output specification of the pack meets the DC requirements above, is CE/FCC approved and has the suitable single-pin 5.5 X 2.1 mm plug, then a MinIT can be powered appropriately.

The MinIT has Wi-Fi Hotspot capabilities so it can be co-ordinated by MinKNOW as a wireless device, which can be used to control the attached MinION Mk 1B. The Wi-Fi connection can be configured like any other wireless connection.

Below are the details on how the MinIT can be connected to a wireless enabled device to control MinKNOW and a MinION Mk 1B.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network through the wireless or wired connections. The network contains the data folder.

To access the MinIT on the Wi-Fi network, enter the below username and password in the appropriate tabs as shown in the below window.

The MinIT has Wi-Fi Hotspot capabilities so it can be co-ordinated by MinKNOW as a wireless device, which can be used to control the attached MinION Mk 1B. The Wi-Fi connection can be configured like any other wireless connection.

Below are the details on how the MinIT can be connected to a wireless enabled device to control MinKNOW and a MinION Mk 1B.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network, both through the wireless and wired connections.

The MinIT has Wi-Fi Hotspot capabilities so it can be co-ordinated by MinKNOW as a wireless device, which can be used to control the attached MinION Mk 1B. The Wi-Fi connection can be configured like any other wireless connection.

Below are the details on how the MinIT can be connected to a wireless enabled device to control MinKNOW and a MinION Mk 1B.

There are several options to connect to your MinIT. These are:

• Default Folder browser for your OS - e.g. \\mt-100007
• Connection Manager on the MinKNOW software

Advanced users

• Secure Shell access - ssh minit@mt-100007 in a terminal

To connect to the device, download the software 'MinKNOW Stand Alone GUI' for your operating system on the Software Downloads page.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network through the wireless or wired connections. The network contains the data folder.

To access the MinIT on the Wi-Fi network, enter the below username and password in the appropriate tabs as shown in the below window.

Once the MinION Mk 1B is plugged into the USB 2.0 port in the MinIT, there are four options:

1. Hardware check 2. Flow cell check 3. Starting a sequencing run 4. Post-run basecalling

These are detailed below:

1. Hardware check

The Configuration Test Cell (CTC) is used for a hardware check that verifies the connections and that the devices are correctly functioning. A number of CTCs are provided with all the sequencing platforms sold by Oxford Nanopore Technologies. The user will also be instructed to check the hardware in the Quick Start Guide that comes with the MinIT.

You can find instructions for how to run a hardware check in the MinION Mk1B installation and configuration protocol.

2. Flow Cell Check

A flow cell has a warranty for a minimum number of pores, where the flow cell can be replaced if the flow cell does not meet this. The Flow Cell Check will quantify the number of functional pores and this check should be performed before the user starts the sequencing experiment.

Instructions on how to run a flow cell check can be found in the Flow Cell Check protocol.

3. Starting a sequencing run

An option exists where the user may have performed the Flow Cell Check and wants to run a sequencing experiment.

The flow cell should remain in the MinION Mk 1B, once the Platform QC has been completed, if the user intends to run a sequencing experiment shortly afterwards. The flow cell should be primed, the library loaded, and the experiment initiated with the flow cell in the MinION Mk 1B, as described in the Oxford Nanopore Technology protocols.

Instructions on how to start a sequencing experiment can be found in the 'Starting a sequencing run' section of the MinKNOW protocol.

4. Post-run basecalling

The MinIT can be used to re-basecall data generated from a nanopore experiment. The input is .fast5 files, containing raw data. The output is in a FASTQ format, containing the basecalled sequence with an associated quality score. Please use the MinKNOW protocol and follow the instructions in Post-run analysis, Post-run basecalling to re-basecall your .fast5 files.

There are several options to connect to your MinIT. These are:

• Default Finder for macOS - e.g. MT-100007
• Connection Manager on the MinKNOW software

Advanced users

• Secure Shell access - ssh minit@mt-100007 in a terminal

To connect to the device, download the software 'MinKNOW Stand Alone GUI' for your operating system on the Software Downloads page.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network, both through the wireless and wired connections.

Once the MinION Mk 1B is plugged into the USB 2.0 port in the MinIT, there are four options:

1. Hardware check 2. Flow cell check 3. Starting a sequencing run 4. Post-run basecalling

These are detailed below:

1. Hardware check

The Configuration Test Cell (CTC) is used for a hardware check that verifies the connections and that the devices are correctly functioning. A number of CTCs are provided with all the sequencing platforms sold by Oxford Nanopore Technologies. The user will also be instructed to check the hardware in the Quick Start Guide that comes with the MinIT.

You can find instructions for how to run a hardware check in the MinION Mk1B installation and configuration protocol.

2. Flow Cell Check

A flow cell has a warranty for a minimum number of pores, where the flow cell can be replaced if the flow cell does not meet this. The Flow Cell Check will quantify the number of functional pores and this check should be performed before the user starts the sequencing experiment.

Instructions on how to run a flow cell check can be found in the Flow Cell Check protocol.

3. Starting a sequencing run

An option exists where the user may have performed the Flow Cell Check and wants to run a sequencing experiment.

The flow cell should remain in the MinION Mk 1B, once the Platform QC has been completed, if the user intends to run a sequencing experiment shortly afterwards. The flow cell should be primed, the library loaded, and the experiment initiated with the flow cell in the MinION Mk 1B, as described in the Oxford Nanopore Technology protocols.

Instructions on how to start a sequencing experiment can be found in the 'Starting a sequencing run' section of the MinKNOW protocol.

4. Post-run basecalling

The MinIT can be used to re-basecall data generated from a nanopore experiment. The input is .fast5 files, containing raw data. The output is in a FASTQ format, containing the basecalled sequence with an associated quality score. Please use the MinKNOW protocol and follow the instructions in Post-run analysis, Post-run basecalling to re-basecall your .fast5 files.

The MinKNOW protocol describes how to install, run and interpret MinKNOW parameters during a sequencing experiment. The protocol can be found in the MinKNOW protocol.

There are several options to connect to your MinIT. These are:

• Default Folder browser for Linux - e.g. smb://mt-100007
• Connection Manager on the MinKNOW software

Advanced users

• Secure Shell access - ssh minit@mt-100007 in a terminal

Please ensure you have downloaded the 'MinIT Software' for your operating system from the Software Downloads page.

To access your MinIT, 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://mt-100007`

in the window shown below.

Clicking Enter in this panel, will enable access to the MinIT's data folder.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network through the wireless or wired connections. The network contains the data folder.

To access the MinIT on the Wi-Fi network, enter the below username and password in the appropriate tabs as shown in the below window.

Once the MinION Mk 1B is plugged into the USB 2.0 port in the MinIT, there are four options:

1. Hardware check 2. Flow cell check 3. Starting a sequencing run 4. Post-run basecalling

These are detailed below:

1. Hardware check

The Configuration Test Cell (CTC) is used for a hardware check that verifies the connections and that the devices are correctly functioning. A number of CTCs are provided with all the sequencing platforms sold by Oxford Nanopore Technologies. The user will also be instructed to check the hardware in the Quick Start Guide that comes with the MinIT.

You can find instructions for how to run a hardware check in the MinION Mk1B installation and configuration protocol.

2. Flow Cell Check

A flow cell has a warranty for a minimum number of pores, where the flow cell can be replaced if the flow cell does not meet this. The Flow Cell Check will quantify the number of functional pores and this check should be performed before the user starts the sequencing experiment.

Instructions on how to run a flow cell check can be found in the Flow Cell Check protocol.

3. Starting a sequencing run

An option exists where the user may have performed the Flow Cell Check and wants to run a sequencing experiment.

The flow cell should remain in the MinION Mk 1B, once the Platform QC has been completed, if the user intends to run a sequencing experiment shortly afterwards. The flow cell should be primed, the library loaded, and the experiment initiated with the flow cell in the MinION Mk 1B, as described in the Oxford Nanopore Technology protocols.

Instructions on how to start a sequencing experiment can be found in the 'Starting a sequencing run' section of the MinKNOW protocol.

4. Post-run basecalling

The MinIT can be used to re-basecall data generated from a nanopore experiment. The input is .fast5 files, containing raw data. The output is in a FASTQ format, containing the basecalled sequence with an associated quality score. Please use the MinKNOW protocol and follow the instructions in Post-run analysis, Post-run basecalling to re-basecall your .fast5 files.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network, both through the wireless and wired connections.

There are several options to connect to your MinIT. These are:

• Default Folder browser for Linux - e.g. smb://mt-100007
• Connection Manager on the MinKNOW software

Advanced users

• Secure Shell access - ssh minit@mt-100007 in a terminal

Please ensure you have downloaded the 'MinIT Software' for your operating system from the Software Downloads page.

To access your MinIT, 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://mt-100007`

in the window shown below.

Clicking Enter in this panel, will enable access to the MinIT's data folder.

Username: minit Password: minit

Note: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.

Below shows the window that is displayed to access the MinIT network through the wireless or wired connections. The network contains the data folder.

To access the MinIT on the Wi-Fi network, enter the below username and password in the appropriate tabs as shown in the below window.

MinIT basecalls data from the MinION Mk 1B, via integrated Guppy in MinKNOW. .fast5 and FASTQ files are output and stored locally on the MinIT in the Data folder.

This folder and the output files can be accessed through the steps below.

MinIT basecalls data from the MinION Mk 1B, via integrated Guppy in MinKNOW. .fast5 and FASTQ files are output and stored locally on the MinIT in the Data folder.

This folder and the output files can be accessed through the steps below.

MinIT basecalls data from the MinION Mk 1B, via integrated Guppy in MinKNOW. .fast5 and FASTQ files are output and stored locally on the MinIT in the Data folder.

This folder and the output files can be accessed through the steps below.

To access your data using a Secure Shell (SSH) terminal, please learn how to SSH into your device using the instructions under Advanced Settings in this document.

To access your data using the Terminal, please learn how to access your device using the instructions under Advanced Settings in this document.

MinIT basecalls data from the MinION Mk1B, via integrated Guppy in MinKNOW. .fast5 and FASTQ files are output and stored locally on the MinIT in the Data folder.

Output files can be accessed and transferred thorugh the steps below.

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

Oxford Nanopore Technologies will post a release note about new software or updates to the MinIT via the Nanopore Community.

We urge users to update as soon as reasonably possible after the release has been made available.

Note: Please check the information for firewall access to the necessary IP addresses and ranges in the section above.

The MinIT Administrator (Admin) Interface has several features to co-ordinate the device. There are brief descriptions on the features of the Admin interface - each has an ability to configure the MinIT, which enables portability, upgrades and management of the system.

1. Device Settings - The devices can be shutdown and rebooted from this page and settings for the time and date can be altered. Disk space can be managed and peripherals may also be added and ejected from here. 2. Software - Users are able to download the latest software updates from this page. The option to update will only appear when an update is available. 3. File Manager - Stored data on the device can be managed and transferred. 4. Help - Device logs can be exported using the Export Logs function. Device tutorials can be reviewed here. 5. Network Settings - Users are able to confirm and change connections between Ethernet, hotspot and WiFi connection. 6. Account Settings - Users are able to log out of their account.

The Admin interface provides the central location for configuring your MinIT. Once the MinIT network securities have been entered and accessed, there are multiple options to control the MinIT to suit the user's needs.

MinIT is a very high specification computer and requires managed shutdown and reboot processes. The shut-down and reboot processes are controlled by the user in the System panel. The procedure and expected screen for Shutdown and Reboot are detailed below on this page.

To configure a 'Shutdown' procedure:

1. Navigate to Device Settings and select Shutdown.
2. Wait for the system to load the Shutdown screen.
3. Select Shutdown.

The window above is shown once the Shutdown option is selected in the System panel.

To configure a 'Reboot' procedure:

1. Navigate to Device Settings and select Reboot.
2. Wait for the system to load the Reboot screen.
3. Select Reboot.

The window above is shown once the Reboot option is selected in the System panel.

MinKNOW, and its components, are the software on MinIT and can run a MinION Mk 1B to attain basecalled data. The software of the system is described in more detail, in the Technical Document, here.

There is an interface for software upgrades (see below for instructions on how to update software on the MinIT). It should be known which revision is installed on your MinIT (for FAQ, troubleshooting, etc.) and this can be found under the in the Software panel:

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  

Oxford Nanopore Technologies will post a release note about new software or updates to the MinIT via the Nanopore Community.

We urge users to update as soon as reasonably possible after the release has been made available.

Note: Please check the information for firewall access to the necessary IP addresses and ranges in the section above.

The wired connection is co-ordinated through the RJ45 port (i.e. Ethernet). It allows access to a network and the internet, if connected to this network.

More information will be available for the 'Wired Connection' soon.

More information will be available for the wireless connection shortly.

More information will be available for the 'System Storage' shortly.

Data storage on the MinIT is an advantage for remote sequencing on a MinION Mk 1B and MinIT combination. The ability to store 450+ GB of data facilitates sequencing and storage of data from more than one experiment.

A sequencing experiment can yield tens of gigabits of data, so it is recommended that the user transfers the basecalled data from the data folder on the MinIT to a long term storage solution or larger scale SSD.

For instructions on how to transfer data, see the relevant sections of this protocol, prefixed 'Data transfer on MinIT - for [your operating system]'.

The Data storage capabilities can be seen on the Admin interface. Used and available data storage can be seen from the Admin interface. Here the used storage capacity (left, 71) and the total (right, 459) can as a proportion of the total capacity.

The date and time panel allow you to configure Time Zones, System Time and System Date.

To configure the time zone, date and time, follow the below instructions:

1. Navigate to Device Settings.

2. Select Change Time and Date in the Time and Date panel and save.

3. Select the Time zone from the drop down menu and save.

The MinIT has two interfaces that we support for data transfer. These are the:

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

Networking with MinIT. Blue lines indicate a connection via the internet. The black line indicates a wired connection. The curved waves indicate a wireless connection. The computer on the LAN (B.) can be used to update MinIT - this is the supported method. You can configure MinIT using the Wi-Fi connected device (A.), however, network compatibility issues may inhibit the updating of your MinIT.

Internet connection:

The suggested update method considers a configuration that requires an ethernet connection to the Local Area Network (LAN) from the MinIT. The LAN is connected to the internet, which enables updating of MinKNOW on the MinIT.

Interface connection:

An interface, such as a laptop/mobile device/computer, can be wirelessly connected to the MinIT (i.e. MinIT in Hotspot mode). Alternatively, the MinIT may be accessed and controlled by a computer on the LAN.

Note: Other configurations exist:

• Ethernet-desktop/laptop computer to control the MinIT - no internet
• MinIT 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 2.0/3.0 ports, however, Oxford Nanopore Technologies cannot advise or support this use.

The latter three suggestions are not supported uses of MinIT's technology by Oxford Nanopore Technologies.

If you need to do configure your device, using parameters that are not available through the Admin interface, you will need to connect via an SSH terminal:

1. Connect to the MinIT using the instructions that are specific for your operating system. e.g. The Wi-Fi Single Sign-on (SS)ID is the MinIT serial number e.g. mt-100007 and the password for the access point is WarmButterflyWings98.
2. Connect to the MinIT using an SSH client. The Hostname is the serial number of the MinIT or IP address by which the MinIT is connected to your device e.g. Wi-Fi or Ethernet.

If you have a Linux computer, then an SSH client, called SSH, is already available. For Windows, we recommend Bitvise for SSH and data transfer or PuTTY to just SSH. A program called Terminal is already installed on macOS that can be used for SSH access.

To SSH in using a terminal, you should:

1 - Enter default username and password in the terminal or Bitvise/PuTTY GUI. These are:

Username: minit Password: minit

Note: You will be prompted for these in the terminal.

2 - To access the MinIT by the terminal, you must enter the command:

ssh [username]@[MinIT serial number] or ssh [username]@[IP address of MinIT]

Note: The username is minit and you can enter the hostname as

1. the MinIT serial number e.g. mt-100007 or
2. the Wi-Fi/Ethernet connection IP address e.g. 10.42.0.1 for a Wi-Fi link or as indicated by the IP address shown in the Admin interface (as of MinKNOW 19.12)

Note: Also, if using Bitvise or PuTTY, you will already be using SSH, once you have logged in via the software's GUI.

If you want to enable static IP addressing on the Ethernet port, then:

  sudo nmcli c down dhcp
  sudo nmcli c up static

If you want to enable dynamic IP addressing on the Ethernet port, then:

  sudo nmcli c down static
  sudo nmcli c up dhcp

The default IP address for the static profile is 192.168.0.1/24. The IP address can be changed along with any other parameter of the connection using the editor:

  sudo nmcli c edit static

The default password should be changed at the earliest possibility to ensure the security of your MinIT.

To change the password.

1. Login to the minit using username and password minit in the SSH/Terminal.
2. Use the command passwd to provide the necessary options for changing the default passsword.
3. The existing password is minit; however, please record your new password safely, as if it is forgotten the user will have to perform a factory reset and risk losing data or risk losing access to the device.

After installing or updating ont-minit-release, the MinIT will be setup to access the Nanopore Community repo. To pull from this repo:

  sudo apt update
  sudo apt install ont-minit-release

To install and run Guppy on MinIT, you can consult the Guppy protocol once support is provided.

All output is written to /data by default which is located on the internal SSD of the MinIT.

If you plug in a USB hard drive, it should be available via /media/usb

The output directories can be changed. To change the output directory:

1. Edit the MinKNOW configuration file:

   sudo vim /opt/ONT/MinKNOW/conf/user_conf

2. Change the output directory file - you should change base from /data to if you only want the data to move from the dirs to different media.

3. Restart the MinIT

To move files on and off the MinIT, you can use the pscp command. You can do this by following the instructions below:

1. Enter the terminal.
2. Enter the pscp command as detailed in the excerpt from www.ssh.com, using the MinIT server and hostname (e.g.minit@mt-100007), file name, its directory, the directory you wish to copy to.

To receive a file from a server: pscp [options] [user@]host:source target So to copy the file /etc/hosts from the server example.com as user fred to the file >c:\temp\example-hosts.txt, you would type: pscp fred@example.com:/etc/hosts c:\temp\example-hosts.tx

e.g. minit@mt-100007:/data/basecalled data [full directory path you wish to copy the file to]

Note: For more help, follow the instructions for PuTTY

1. Open a terminal window

2. Connect to the machine using the sftp command below. sftp -o ServerAliveInterval=10 -o TCPKeepAlive=no -i /Users/$(whoami)/Downloads/[Device Name]

3. To input the path to file you wish to move, simply drag the file onto to the terminal window. This path may be different than above depending on where you saved the file.

4. Once connected download the script output files with the get command:

sftp> get [File Name]

The logs record the command-line information that the MinIT is using to run MinKNOW, the Admin interface and the operating system, Linux.

These records can be used by Technical Support at Oxford Nanopore Technologies to diagnose errors and crashes that occur on users' MinITs.

To access these files using the terminal/SSH, follow the commands here and in Data transfer - SSH sections.

1. Open a terminal
2. Login, if you have not already done so, using pscp or sftp and username: minit and password: minit.
3. Using the relevant commands for sftp or pscp, copy over the file /var/log/MinKNOW to your computer/laptop.
4. You will then find your logs in the location identified in the file transfer command.