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.

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

gdb multiarch
(gdb) set architecture armv7
(gdb) target extended-remote localhost:3333
(gdb) info registers
r0             0x1ff               511
r1             0x8000000           134217728
r2             0x1                 1
r3             0x20070e38          537333304
r4             0x3e8               1000
r5             0x2711              10001
r6             0x81d8c             531852
r7             0x93cdc71           154983537
r8             0x2007002c          537329708
r9             0xd844d7c0          -666576960
r10            0x2358288a          592980106
r11            0x314f2ac3          827271875
r12            0xa8                168
sp             0x20087fd8          0x20087fd8
lr             0x8090b             526603
pc             0x8090a             0x8090a
xPSR           0x81000000          -2130706432
msp            0x20087fd8          0x20087fd8
psp            0x4921e0e0          0x4921e0e0
primask        0x0                 0
basepri        0x0                 0
faultmask      0x0                 0
control        0x0                 0

Due bootloader

Microchip ATSAM3X8E