Atmel Studio is an Integrated Development Environment (IDE) for programming and debugging AVR and SAM applications with JTAG, aWire, SPI, PDI, TPI, and SWD interface selected in Windows® environments.
For AVR or SAM devices programmed with Atmel-ICE, use the "Device programming" option integrated in the Atmel Studio IDE or the command line utility called atprogram provided by Atmel Studio. During the Atmel Studio installation a shortcut called Atmel Studio 7.0 (version number depending on the specific Atmel Studio version installed) 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 Studio 7.0/atbackend.