ClamAV is great too. If you don’t want to have to use the GUI interface, do this (assuming you already have clamav from the repository, which the live CD will probably have — if you don’t have it, “sudo apt-get install clamav” will install it):

sudo freshclam (to update to the newest signature)

Make sure your drive is mounted wherever it normally gets mounted.

sudo clamscan –infected –bell –move=/path/to/virus/vault -r /path/to/mounted/drive

The –infected makes it only print out when it finds an infected file. Omit it if you want to watch as it displays every single file on your drive. –bell makes it beep when it finds a virus. –move= sends all infected files to a specific folder (what I’m calling a “virus vault” here). -r recurses through all subfolders.

There are a lot more options than presented here. clamscan –help will list most of the relevant ones.