CLC Server Command Line Tools

by QIAGEN Aarhus A/Sv26.0.2

QIAGEN.CLCServerCommandLineTools

Last updated Apr 28, 2026

A command line client for the QIAGEN CLC Genomics Server.

Install with winget

$ winget install --id QIAGEN.CLCServerCommandLineTools --exact --version 26.0.2

Run in Command Prompt, PowerShell, or Windows Terminal. Prompts for any agreements.

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About

QIAGEN CLC Server Command Line Tools provides a command line client for the QIAGEN CLC Genomics Server. This client software can be used to launch bioinformatics analyses including workflows, import and export data, and carry out utility operations such as moving, renaming, and deleting data. Commands can be run directly or included in scripts.

Installers · v26.0.2

Architecture	Type	Scope	Install	Download
x64	exe	machine		Direct

Copy a command tailored to that specific architecture, type, and scope - useful when winget would otherwise pick a different default.

Related apps

CLC Main WorkbenchQIAGEN Aarhus A/S
QIAGEN.CLCMainWorkbenchv26.0.2
DNA, RNA and protein sequence data analysis.
CLC Genomics WorkbenchQIAGEN Aarhus A/S
QIAGEN.CLCGenomicsWorkbenchv26.0.2
Access all the tools you need for data analysis with our comprehensive solution. Start shifting your focus from data to discovery and take advantage of NGS workflows, interpretation and visualization.

Frequently asked questions

How do I install CLC Server Command Line Tools on Windows?

Open Windows Terminal, PowerShell, or Command Prompt and run: winget install --id QIAGEN.CLCServerCommandLineTools --exact --version 26.0.2. winget downloads the installer from QIAGEN Aarhus A/S and runs it. Requires Windows 10 (1809+) or Windows 11.

How do I install CLC Server Command Line Tools silently for unattended deployment?

Add --silent and accept the agreements upfront: winget install --id QIAGEN.CLCServerCommandLineTools --exact 26.0.2 --silent --accept-package-agreements --accept-source-agreements. This is the variant Intune, Configuration Manager, and other deployment tools should use.

How do I uninstall CLC Server Command Line Tools via winget?

Run: winget uninstall --id QIAGEN.CLCServerCommandLineTools --exact. Add --silent for unattended uninstalls. winget will use the registered uninstaller from CLC Server Command Line Tools's Apps & Features entry.

Is CLC Server Command Line Tools free?

CLC Server Command Line Tools is distributed under Proprietary. Refer to the publisher for the full license terms - Wingetly itself does not charge for installation.

Does CLC Server Command Line Tools work on Windows 10?

Yes, as long as your Windows 10 build supports winget (1809 or newer). winget ships with App Installer on Windows 10/11 and pulls CLC Server Command Line Tools directly from the publisher.

How do I keep CLC Server Command Line Tools up to date?

Run winget upgrade --id QIAGEN.CLCServerCommandLineTools --exact, or winget upgrade --all to update everything winget tracks. We index 4 versions of CLC Server Command Line Tools from microsoft/winget-pkgs.

Recent versions

26.0.2latest
26.0.1
25.0.3
25.0.2