Arria V GZ FPGA firmaware modification for an ADC application

Have you looked through Altera's transceiver technology jesd204b (https://www.altera.com/solutions/technology/transceiver/jesd204b/je-index.html) pages. There is plenty of information there.

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my plan is to modify the firmware of the FPGA...

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Do you have this 'firmware'? What language is it written in? Are you familiar with it?

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What is the JESD204B IP license?

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You will need the license to use the JESD204B IP that Altera have. This will be a big portion of well tested, proven code. You can either use that code or write your own.

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I'm totally new to the consepts and practicalities of FPGA programming and hardware.

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Dare I ask what your experience is?

I certainly don't want to put you off but, depending on your answers to these questions, this could end up being a pretty difficult exercise.

Cheers,

Alex