SPAdes (St. Petersburg genome assembler) is a de novo assembler, intended for assembling small genomes, including standard isolates and single-cell MDA bacteria assemblies. SPAdes is available in Geneious R10.1 and later.
Normally SPAdes can only run on a 64-bit Linux system or Mac OS, but within Geneious it is possible to run SPAdes on a 64-bit Windows 10 system if you install Windows Subsystem for Linux, following the setup instructions below. You must be using Windows 10 Pro with all recent updates installed.
Setup instructions to run SPAdes on Windows 10
- Run PowerShell as Admin – from the Start menu, right-click on Windows PowerShell > Windows PowerShell, then select 'Run as Administrator'.
- At the terminal prompt, type 'Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux'.
- Wait for Windows Subsystem for Linux installation to complete, then restart your computer if Windows prompts you to do so.
- Open the Microsoft Store app, and search for and install 'Ubuntu 16.04 LTS'.
- 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 10.
- Open Ubuntu 16.04 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).
Note: If you are using Geneious 10.2.6 or earlier, you need to run the following additional command after creating your Ubuntu username and password:
sudo bash -c "ln -s /usr/bin/python3 /usr/local/bin/python"
You can now close Ubuntu, and you should be able to run SPAdes on your Windows 10 machine (until you have run SPAdes for the first time the message about setting this up will still show, but it should now run if you click 'OK').
Will SPAdes work with other Linux distributions from the Microsoft Store?
The Microsoft Store now offers multiple Linux distributions for Windows 10, however, SPAdes in Geneious is only supported on Ubuntu 16.04 (recommended, Geneious 10.1 and later) and 18.04 (Geneious Prime 2019.2 and later). If you wish to use Ubuntu 18.04, you’ll need to perform additional steps after installing Ubuntu and setting a username and password:
- Open Ubuntu 18.04 LTS from the Start menu.
- Install the distutils package for Python 3 with the following command, entering your Ubuntu password when prompted: 'sudo apt-get update && sudo apt-get install python3-distutils'.