The Due is a larger form factor Arduino board containing a ATSAM3X8E ARM Cortex-M3 processor running at 84MHz.

There are two USB connectors on this board. One is labelled the native port which is a direct connection to the processor. This allows the MCU to become a USB device in its own right. The other port called the programming port connects to a serial bridge for updating the firmware and it also allows regular UART communication.

SAM BA is the ROM based bootloader found on the processor and is connected to via the programming port.

BOSSA

JTAG utilises the miniature header and can be used with the JLink EDU Mini.

Segger J-Link

With an adapter the Olimex UCD USB H can also be utilised

openocd -f "interface/ftdi/olimex-arm-usb-ocd-h.cfg" -c "adapter speed 4000" -c "transport select jtag" -f "target/at91sam3XXX.cfg"
Open On-Chip Debugger 0.12.0-rc2+dev-00012-g4e077fdda (2022-11-12-16:05)
Licensed under GNU GPL v2
For bug reports, read
        http://openocd.org/doc/doxygen/bugs.html
adapter speed: 4000 kHz

jtag
cortex_m reset_config sysresetreq

Info : Listening on port 6666 for tcl connections
Info : Listening on port 4444 for telnet connections
Info : clock speed 500 kHz
Info : JTAG tap: sam3.cpu tap/device found: 0x4ba00477 (mfg: 0x23b (ARM Ltd), part: 0xba00, ver: 0x4)
Info : [sam3.cpu] Cortex-M3 r2p0 processor detected
Info : [sam3.cpu] target has 6 breakpoints, 4 watchpoints
Info : starting gdb server for sam3.cpu on 3333
Info : Listening on port 3333 for gdb connections
^Cshutdown command invoked

Due bootloader

Microchip ATSAM3X8E