standalone native USB port?


I am trying to integrate an Arduino Due into the main PCB for our custom project. Instead of placing a "breakout" board onto the main PCB, I thought: "why not integrate the MCU directly?"

I plan on simulating all of the necessary hardware onto our main PCB. My question is, is the 16U2 secondary MCU used for flash erasing absolutely essential to the operation of the Due?

From what I researched, the sole purpose of the 16U2 is to provide a reliable way of hard-clearing the flash on the main MCU. So if I were to implement only the native USB onto my design, will there ever be a case where the flash cannot be cleared?


It mentions a manual reset which would make this possible:

"The SAM3X microcontroller differs from AVR microcontrollers because the flash memory needs to be erased before being re-programmed. A manual procedure would involve holding the erase button for a second, pressing the upload button in the IDE, then the reset button.

Because a manual erase-flash procedure is repetitive, this is managed automatically by both USB ports, in two different ways:"

Can this procedure be done with the native port? So if my sketch causes the chip to crash, I can follow the above procedure to upload a new sketch with the native port?

Also would the IDE recognize that I am doing this? For example, it goes through all of these steps automatically under normal uploading conditions. So if I do this manual way, would it know its in manual mode or would it continue with the series of automatic steps and reset the MCU by itself at the end, so that I don't have to press the reset button after?

Thanks for any help,


as seen from another thread werid error - No device found - Arduino Due - Arduino Forum my programming port is non-functional
i have been programming via the Native port by

  1. pressing erase
  2. pressing reset
  3. uploading sketch ..

PITA but it works ...