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AVRdude

AVRDUDE is a command line tool to program AVR chips. It runs in the background of the Arduino IDE. Sometimes it is necessary to erase a chip or set the fuse bits that's when the AVRdude comes handy.

Dokumentations:
http://www.nongnu.org/avrdude/user-manual/avrdude.html
Command description:
http://www.nongnu.org/avrdude/user-manual/avrdude_4.html

avrdude -C <arduino-ide-folder>/hardware/tools/avrdude.conf -v -p <partno> -c <programmer> -P <port> -b 115200 -U flash:w:<full_path_to_hex>:i

-C <config-file> specify location of configuration file -v verbose output-v, in case you want to debug something -p <partno> specify AVR devicee could be atmega328p or m8u, … -c <programmer> specify programmer type could be stk500v1 or stk500v2, … -P <port> specify connection port could be /dev/ttyACMx (Linux $ ls /dev), or COMx (Win) -b <baudrate> override RS-232 baud rate -U <memtype>:r|w|v:<filename>[:format] 

                 memory operation specification,
                 the <memtype> is either flash or eeprom
                 r|w|v means r (read) w (write) or v (verify)

<full_path_to_hex> is the hex filename and location

ATmega32U4
To erase the chip: 

sudo avrdude -p m32u4 -c stk500v2 -P /dev/ttyACM0 -e -F

ATmega328p
To erase the chip: 

sudo avrdude -p m328p -c stk500v2 -P /dev/ttyACM0 -e -F

ATmega168
set the fuse bits: 

avrdude -c stk500v2 -p m168 -P /dev/ttyACM0 -B 6 -v -U lock:w:0x3f:m -U lfuse:w:0xff:m -U hfuse:w:0xdf:m -U efuse:w:0x0:m

Atmega8u2
It is the chip for serial to USB on the Arduino Uno and on the Usb2Serial board.

<!> On the Arduino Usb2Serial Light Board the ISP header is marked wrong, pin 1 is the nearest one to the Atmega8u2 chip <!>

Burning Serial to USB: 

sudo avrdude -C /usr/share/arduino/hardware/tools/avrdude.conf -p m8u2 -c stk500v2 -P /dev/ttyACM0 -b115200 -U flash:w:Arduino-usbserial-uno.hex:i

Burning Serial to Midi: 

sudo avrdude -C /usr/share/arduino/hardware/tools/avrdude.conf -p m8u2 -c stk500v2 -P /dev/ttyACM0 -b115200 -U flash:w:MIDI_Firmware/Arduino-usbmidi-0.2.hex:i

Burning Serial to USB on Sparkfun Atmega8u2 Breakout: 

sudo avrdude -p m8u2 -c stk500v2 -P /dev/ttyACM0 -U flash:w:Arduino-usbserial-uno.hex:i