I have a custom board using a SAMD21 microcontroller (as used in Arduino Zero and other dev boards).

After soldering, the chip is blank and a bootloader is useful to upload code via the USB connection. 

I found an excellent (as always) tutorial by Adafruit using a JLink probe to upload their custom bootloader here : https://learn.adafruit.com/how-to-program-samd-bootloaders/overview

Unfortunately, directions are only provided for a Windows computer, using Atmel Studio.

Here is how to do it using the JLink command line software under Linux (and it should work with Mac as well).

To enable/disable the bootloader protection, I found very useful information here : https://roamingthings.de/posts/use-j-link-to-change-the-boot-loader-protection-of-a-sam-d21/

You should create two files with the info from the above post :

File SAMD_set_bootloader_protection_8k.mot :

S214804000FAC7E0D85DFCFFFFFFFFFFFFFFFFFFFF63
S9030000FC

File SAMD_clear_bootloader_protection.mot :

S214804000FFC7E0D85DFCFFFFFFFFFFFFFFFFFFFF5E
S9030000FC

In the same directory, download the Adafruit bootloader from https://learn.adafruit.com/how-to-program-samd-bootloaders/setup

So here is the complete process to burn a bootloader to a blank SAMD21 chip :

• Go to the directory where you put the two files above and the bootloader binary

cd ATSAMD21_Bootloader

• Start JLinkExe

$ JLinkExe
SEGGER J-Link Commander V6.32h (Compiled Jul  5 2018 18:15:02)
DLL version V6.32h, compiled Jul  5 2018 18:14:58

Connecting to J-Link via USB...O.K.
Firmware: J-Link Lite-Cortex-M V8 compiled Sep 15 2016 12:05:01
Hardware version: V8.00
S/N: 518006749
License(s): GDB
VTref=3.313V


Type "connect" to establish a target connection, '?' for help

•  Connect to the microcontroller. You have to specify the device type, SWD interface and you can use the default interface speed.

J-Link>connect
Please specify device / core. : ATSAMD21G18
Type '?' for selection dialog
Device>atsamd21g18
Please specify target interface:
  J) JTAG (Default)
  S) SWD
TIF>s
Specify target interface speed [kHz]. : 4000 kHz
Speed>
Device "ATSAMD21G18" selected.


Connecting to target via SWD
InitTarget()
Found SW-DP with ID 0x0BC11477
Scanning AP map to find all available APs
AP[1]: Stopped AP scan as end of AP map has been reached
AP[0]: AHB-AP (IDR: 0x04770031)
Iterating through AP map to find AHB-AP to use
AP[0]: Core found
AP[0]: AHB-AP ROM base: 0x41003000
CPUID register: 0x410CC601. Implementer code: 0x41 (ARM)
Found Cortex-M0 r0p1, Little endian.
FPUnit: 4 code (BP) slots and 0 literal slots
CoreSight components:
ROMTbl[0] @ 41003000
ROMTbl[0][0]: E00FF000, CID: B105100D, PID: 000BB4C0 ROM Table
ROMTbl[1] @ E00FF000
ROMTbl[1][0]: E000E000, CID: B105E00D, PID: 000BB008 SCS
ROMTbl[1][1]: E0001000, CID: B105E00D, PID: 000BB00A DWT
ROMTbl[1][2]: E0002000, CID: B105E00D, PID: 000BB00B FPB
ROMTbl[0][1]: 41006000, CID: B105900D, PID: 001BB932 MTB-M0+
Cortex-M0 identified.

• Clear bootloader protection fuse

J-Link>loadfile SAMD_clear_bootloader_protection.mot
Downloading file [SAMD_clear_bootloader_protection.mot]...
Comparing flash   [100%] Done.
Erasing flash     [100%] Done.
Programming flash [100%] Done.
Verifying flash   [100%] Done.
J-Link: Flash download: Bank 1 @ 0x00804000: 1 range affected (16 bytes)
J-Link: Flash download: Total time needed: 0.050s (Prepare: 0.037s, Compare: 0.002s, Erase: 0.000s, Program: 0.003s, Verify: 0.000s, Restore: 0.006s)
O.K.

• Reset the target

J-Link>r
Reset delay: 0 ms
Reset type NORMAL: Resets core & peripherals via SYSRESETREQ & VECTRESET bit. 

• Upload the bootloader (you may have to change the bin file name).

J-Link>loadbin bootloader-feather_m0-v2.0.0-adafruit.9.bin,0
Downloading file [bootloader-feather_m0-v2.0.0-adafruit.9.bin]...
Comparing flash   [100%] Done.
Verifying flash   [100%] Done.
J-Link: Flash download: Bank 0 @ 0x00000000: Skipped. Contents already match
O.K. 

• Set the bootloader protection fuse

J-Link>loadfile SAMD_set_bootloader_protection_8k.mot
Downloading file [SAMD_set_bootloader_protection_8k.mot]...
Comparing flash   [100%] Done.
Erasing flash     [100%] Done.
Programming flash [100%] Done.
Verifying flash   [100%] Done.
J-Link: Flash download: Bank 1 @ 0x00804000: 1 range affected (16 bytes)
J-Link: Flash download: Total time needed: 0.050s (Prepare: 0.037s, Compare: 0.002s, Erase: 0.000s, Program: 0.003s, Verify: 0.000s, Restore: 0.006s)
O.K.

Now unplug and plug back your board and the SAMD21 should enumerate as a composite USB mass storage device and serial interface.