How do I scan for viruses with ClamAV?

Terminal

At first you have to update the virus definitions with:

sudo freshclam

Then you can scan for viruses.

clamscan OPTIONS File/Folder 

If necessary start with root permissions: sudo clamscan.

Examples:

• To check all files on the computer, displaying the name of each file:

  clamscan -r /
  

• To check all files on the computer, but only display infected files and ring a bell when found:

  clamscan -r --bell -i /
  

• To scan all files on the computer but only display infected files when found and have this run in the background:

  clamscan -r -i / &
  

  Note - Display background process's status by running the jobs command.

• To check files in the all users home directories:

  clamscan -r /home
  

• To check files in the USER home directory and move infected files to another folder:

  clamscan -r --move=/home/USER/VIRUS /home/USER
  

• To check files in the USER home directory and remove infected files (WARNING: Files are gone.):

  clamscan -r --remove /home/USER
  

• To see more options:

  clamscan --help
  

See:

• Latest documentation: PDF | HTML
• ClamAV official Wiki
• Ubuntu Wiki

Graphical User Interface: ClamTK

ClamTk is a frontend for ClamAV. You can install it via Terminal with:

sudo apt-get install clamtk

You can get the latest version from Bitbucket as Debian package.

There is also a PPA (Outdated):

sudo apt-add-repository ppa:landronimirc/clamtk
sudo apt-get update && sudo apt-get install clamtk

Scan Menu: Here you can choose a file, folder or a device for scanning

View Menu:

Quarantine Menu:

Advanced Menu:

Help Menu: Here you can check for updates.

See:

• ClamTk@Sourceforge
• ClamTk Help
• ClamTk FAQ

The accepted answer is a great answer, but every time I reach this page, it's a pain to find the command I want from the clutter of information. So just providing a concise answer to the question:

sudo apt-get install clamav; sudo freshclam

To scan all folders in your computer (except /sys):

clamscan -r -i --exclude-dir="^/sys" --bell / 

To scan specific folders or files, you have to create a file in which you list out which files/folders you want to scan, and tell clamav where to find that file:

clamscan -r -i --bell --file-list=/home/nav/ClamScanTheseFolders.txt

My ClamScanTheseFolders.txt contained:

/media/nav/someFolder1
/media/nav/someFolder2
/opt/someFolder/somefile