Atmel Studio comes with a command-line utility called atprogram that can be used to program targets using the Atmel-ICE. During the Atmel Studio installation, a shortcut called “Atmel Studio7.0 Command Prompt” was created in the Atmel folder on the Start menu. By double-clicking this shortcut, a command prompt will be opened, and programming commands can be entered. The command-line utility is installed in the Atmel Studio installation path in the folder Atmel/Atmel Studio7.0/atbackend/.
atprogram --help