This page describes how to flash a completely new board, for example the 28Pins board which you have built by yourself. Important! This only work with 28Pins board, variant FIXED 5V with 16MHz crystals. If you have your own board with different crystal values, you will need to prepare your own firmware files. Have a look at How to Compile Firmware for 3V3 28Pins Variant.
ATMEL FLIP Software
In this step we are going to change default factory settings of 16U2 microcontroller.
Note: If you do not have ATAVRDRAGON, you can use Arduino or 28Pins with MKII firmware. If you use Arduino, it will require some wiring.
In this step we are going to change 16U2 firmware. After the firmware update 16U2 becomes MKII programmer.
In this step, we will flash the Arduino bootloader into ATMEGA328P through ATMEGA16U2.
In this step we are going to flash Serial to USB firmware into the 16U2. We will use FLIP again.
We are going to upload Arduino "Blink" example to test the board.