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I'm not familiar with the underlying technology of X2Go (namely NX). I keep hearing that it uses ssh, but just for completeness and since I'm paranoid about security: Is there any reason to have to use X2Go through an ssh tunnel? Or does directly connecting to the remote server suffice? I'm talking about connecting to a public server.

The level of security I'm seeking is the same level provided by standard ssh. If that's everything that NX needs (and hence does it under the hood), then probably there's probably no need for a tunnel.

To rephrase: Is there any benefit to using an ssh tunnel for security with X2Go?

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x2go just uses ssh under the hood to connect to the remote machine and you do not set up ssh tunnels manually.
When you refer to directly connecting, assuming a direct X11 connection, this would not be encrypted and theoretically anything like commands and password you enter can be read by third-party. Tunneling the X11 stuff through SSH prevents this security issue.

Another benefit is that you only need to open SSH in any firewalls in between, so if SSH connection is working the x2go connection should work as well.

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