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I'm new to electronics and come from the software side of things.

Now we are working on a project and we need to program a MCU. Since it's an Atmel MCU we had to get a programmer. It is the Atmel-ICE debugger.

So now I was reading on the internet about debugging embedded devices by JTAG and I was wondering if I could just use the programmer for other JTAG operations since there is a JTAG connector shipped with it?

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In theory and from a hardware point of view: Yes. The problem will be, that whatever other tool you are going to use for those "other JTAG operations" (i.e. Boundary Scan testing or JTAG-debugging of other non-Atmel MCUs) is most likely not going to support the Atmel-ICE debugger. Especially if those are commercial tools with an interest in selling their own hardware.

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