Once extracted, you will see a folder containing various files. This is where many Windows users get stuck. You won't find a desktop icon automatically created. Here is how to set it up.

Bioinformatics tools are increasingly used via the command line (CLI). Running FastQC via the Windows Command Prompt or PowerShell gives you more control over input/output directories.

You should see output like:

If FastQC is working, you will see the help menu listing all command-line options.

However, unlike standard software, downloading and "installing" FastQC on Windows isn't always straightforward. It doesn’t come with a fancy installer; it runs via a command line or a simple double-click.