The Pololu USB AVR Programmer Version 2.1 is a very versatile and reliable device that programs ATMEGA AVR devices.

Fetch required binary archive for your computer system and install the utility software to control the special features of the programmer.

Avrdude will be used to perform the actual programming once everything is setup.

tar Jxvf pololu-usb-avr-programmer-v2-1.1.0-linux-rpi.tar.xz
cd pololu-usb-avr-programmer-v2-1.1.0-linux-rpi
sudo ./install.sh

Check that things are operating

$ pavr2cmd -s
Name:                                    Pololu USB AVR Programmer v2.1
Serial number:                           00263944
Firmware version:                        1.02
Programming port:                        /dev/ttyACM1
TTL port:                                /dev/ttyACM2

Settings:
  ISP frequency (kHz):                   114
  Max ISP frequency (kHz):               1714
  Regulator mode:                        auto
  VCC output:                            Disabled
  VCC output indicator:                  Blinking
  Line A function:                       None
  Line B function:                       DTR
  VCC/VDD maximum range (mV):            896
  VCC 3.3 V minimum (mV):                2720
  VCC 3.3 V maximum (mV):                3872
  VCC 5 V minimum (mV):                  4128
  VCC 5 V maximum (mV):                  5856
  STK500 hardware version:               F
  STK500 software version:               2.A

Results from last programming:           N/A

Current status:
  Target VCC (mV):                       0
  Programmer VDD (mV):                   3328
  VDD regulator set point:               3.3 V
  Last device reset:                     Power-on reset

The programmer can either be used in ISP STK500 mode else as a serial UART for a bootloader.

Query a MEGA2560 connecter by ISP.

avrdude -B 5 -c avrisp2 -P `pavr2cmd --prog-port` -p m2560

Product page

User's guide