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How do I set up Windows 10/11 to run SPAdes, Flye, or STAR assemblers?

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The assemblers SPAdes, Flye, and STAR can normally only run on a 64-bit Linux system or Mac OS.  Therefore, to run these on a 64-bit Windows 10 or 11 system you will need to install Windows Subsystem for Linux following the setup instructions below.  

You must be using Windows 10 or newer with all recent updates installed. Furthermore, Geneious Prime 2019.2 or later is required for SPAdes, Geneious Prime 2020.1 and later for Flye, and Geneious Prime 2023 or later for STAR.

Instructions for installing Windows Subsystem for Linux on Windows 10/11 in Geneious 2025 (see note below for older versions).

  1. Run PowerShell as Admin – from the Start menu, right-click on Windows PowerShell Windows PowerShell, then select 'Run as Administrator'.
  2. At the terminal prompt, type 'Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux'.
  3. Wait for Windows Subsystem for Linux installation to complete, then restart your computer if Windows prompts you to do so.
  4. Open the Microsoft Store app, and search for and install 'Ubuntu 22.04 LTS'.
  5. Wait until the installation window disappears (this may take a few minutes). Note: if this step fails, please make sure you have installed all recent updates for Windows.
  6. Open Ubuntu 22.04 LTS from the Start menu. This may take some time as Ubuntu is set up for the first time. You’ll be prompted to create a username and password (these don't need to be the same as your Windows username/password).  
  7. Within Windows Subsystem for Linux , run sudo apt-get update && sudo apt-get install libgomp1

You can then close Ubuntu and you should be able to run SPAdes or Flye on your Windows 10/11 machine (until you have run them for the first time the message about setting this up will still show, but it should now run if you click 'OK').  Note that Flye is an external plugin and must be installed from the Plugins menu before use. 

 

Note for older versions of Geneious:

The compatibility between Spades and Ubuntu is version specific. Please follow the instructions above using the correct version of Ubuntu as listed below:

To run SPAdes on Windows in Geneious Prime 2020-2024 requires Ubuntu 20.04. 

To run SPAdes on Windows in Geneious Prime 2019.1 and earlier requires Ubuntu 16.04. Ubuntu 16.04 is no longer available from the Microsoft App Store. 

 



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