dfu-programmer

device firmware update (DFU) based USB programmer for Atmel chips
  http://dfu-programmer.sourceforge.net/
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A Linux based command-line programmer for Atmel chips with a USB bootloader supporting in-system programming.

This is a mostly Device Firmware Update (DFU)-1.0-compliant user-space application. This program was created because the Atmel FLIP program for flashing devices does not run on Linux and because standard DFU loaders do not work for Atmel chips.