ClamAV is "the (only...) Antivirus" when referring to Linux.
To scan from the cli is very easy:
root@srvr101 [/home/guido]# clamscan -r -v -i --bell > clamscan-guido-infected.log 2>clamscan-guido-error.log &
-r Stands for recursive.
-v Is for verbose.
-i Prints the infected files only.
--bell sounds a bell for every positive result found.
The infected scan result will be put inside the clamscan-guido-infected.log and the standard error log will be written inside clamscan-guido-error.log.
The & will execute the scan on the background and the prompt will allow you to do whatever you wish during the scan.