How to Download and Install MinKNOW for Oxford Nanopore Sequencing

Why MinKNOW Matters in Your Sequencing Workflow

If you’re about to start a run on an Oxford Nanopore device, the first piece of software you’ll meet is MinKNOW. It’s more than a simple driver; it’s the control centre that streams raw signal, monitors pore health, and even performs on‑the‑fly basecalling when you enable it. Getting MinKNOW up and running correctly can be the difference between a smooth data collection session and a night spent troubleshooting.

Below is a practical walk‑through that assumes you have a basic familiarity with command‑line tools but no deep‑dive experience with Nanopore ecosystems. The steps work for Windows, macOS, and the most common Linux distributions.

Check System Requirements Before You Begin

• Supported operating systems: Windows 10 (64‑bit), macOS 10.15+ (Catalina or newer), Ubuntu 18.04/20.04 LTS, and CentOS 7/8.
• Hardware basics: at least 8 GB RAM, a dual‑core CPU, and 10 GB of free SSD space for the software and temporary files.
• GPU (optional): NVIDIA cards with CUDA 10.2+ improve real‑time basecalling speed, but are not mandatory.
• Network: an active internet connection is needed for the initial download and license verification.

Meeting these requirements doesn’t guarantee flawless operation, but it eliminates the most common sources of error.

Create an Oxford Nanopore Community Account

MinKNOW is distributed through the Oxford Nanopore Community portal. If you haven’t already, sign up at community.nanoporetech.com. The registration process asks for basic contact details and a brief description of your intended use (research, clinical, education, etc.). Once your account is active, you’ll receive an email with a verification link—click it, then log in.

Downloading the Correct MinKNOW Package

After logging in, navigate to the “Downloads” section. You’ll see a list of software bundles; the one you need is labelled “MinKNOW” followed by a version number (e.g., 22.05.1). Choose the package that matches your operating system:

• Windows: a .exe installer.
• macOS: a .dmg disk image.
• Linux: a .deb (Debian/Ubuntu) or .rpm (CentOS/RHEL) file.

Tip: If you plan to run multiple devices or need the latest bug fixes, select the “latest stable release” rather than a long‑term support (LTS) version. The portal also offers “beta” builds for early access to new features, but those can be less reliable.

Installing MinKNOW on Windows

1. Double‑click the downloaded .exe file.
2. When prompted, accept the license agreement and choose an installation folder (the default works for most users).
3. During setup, you may be asked whether to install the “MinKNOW GUI” and “Command‑Line Tools.” Keep both checked; the GUI is handy for quick checks, while the CLI is essential for scripting.
4. Finish the wizard and reboot your computer if the installer recommends it.

After the reboot, you’ll find MinKNOW in the Start menu. The first launch will ask you to sign in with your community credentials, which activates your licence.

Installing MinKNOW on macOS

1. Open the .dmg file and drag the MinKNOW icon into your Applications folder.
2. macOS will warn you that the app is from an unidentified developer. Open System Preferences → Security & Privacy, click “Open Anyway,” then confirm.
3. Run MinKNOW from Applications; the program will prompt you for your community login.

If you encounter a “permission denied” error when launching, open Terminal and run chmod +x /Applications/MinKNOW.app/Contents/MacOS/MinKNOW to grant execute rights.

Installing MinKNOW on Linux

Linux users have two main routes: using the package manager or extracting a tarball. The package manager method is simpler and ensures automatic dependency handling.

# For Debian/Ubuntu
sudo dpkg -i minKNOW_22.05.1_amd64.deb
sudo apt-get -f install   # fixes missing dependencies
# For CentOS/RHEL
sudo rpm -i minKNOW-22.05.1.x86_64.rpm

If you prefer a tarball, download the .tar.gz, extract it, and run the included install.sh script. Remember to add the MinKNOW binary directory to your PATH so you can call it from any terminal.

Running a Quick “Hello World” Test

Before you connect a flow cell, it’s wise to verify that MinKNOW can communicate with your hardware. Plug in the device (e.g., MinION Mk1B or GridION) via USB‑C, then launch the GUI. In the “Device” tab you should see the device name and a green “Ready” status.

If the status shows “Disconnected,” double‑check the cable, ensure you have the latest USB drivers installed (Windows) or that the user belongs to the dialout group (Linux). A quick reboot often resolves lingering driver conflicts.

Enabling Real‑Time Basecalling (Optional)

Basecalling translates raw ionic current into nucleotide sequences. MinKNOW offers two paths:

• Guppy integration: install the Guppy basecaller (available separately on the community site) and enable it in the “Basecalling” settings.
• On‑device basecalling: newer flow cells support “Fast Mode” which offloads a portion of the work to the device’s built‑in GPU.

For most labs, starting with Guppy on a dedicated workstation strikes the best balance between speed and reliability.

Troubleshooting Common Issues

• License errors: re‑enter your community credentials or run minKNOW --refresh-license from the command line.
• Device not detected: check that the USB controller is not in “power‑saving” mode; on Windows this can be adjusted in Device Manager under “USB Root Hub – Power Management.”
• GPU not recognized: ensure CUDA drivers match the version bundled with Guppy; reinstalling the NVIDIA driver often clears mismatches.

When in doubt, the MinKNOW log (accessible via the “Help → Show Log” menu) contains timestamps and error codes that are searchable on the Nanopore Community forums.

Keeping MinKNOW Up to Date

Software updates arrive roughly every 4‑6 weeks. The MinKNOW GUI will pop up a notification when a new version is available. You can also schedule automatic checks in the settings pane. Regular updates bring performance tweaks, bug fixes, and support for the latest flow‑cell chemistries, so it’s good practice to stay current.

FAQ

What is MinKNOW and do I need it for every Nanopore run?

MinKNOW is the official control software for Oxford Nanopore devices. It handles pore activation, data acquisition, and optional basecalling. While the hardware can technically generate raw signal without MinKNOW, the software provides essential monitoring tools and is required for most standard workflows.

Can I run MinKNOW without an internet connection?

Initial installation and licence activation need internet access, but once the software is licensed you can operate it offline. Real‑time basecalling with Guppy, however, may still request occasional online checks for updates.

Which operating systems are officially supported?

Oxford Nanopore lists Windows 10 (64‑bit), macOS 10.15+ (Catalina onward), and Ubuntu 18.04/20.04 LTS as fully supported. Community users have reported success on other Linux distributions, but those setups may require extra dependency handling.