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Ixiasoft
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19.3.1.5. Programming the Flash
Programming the flash is done by using quartus_cpf to combine a compiled FPGA image (SOF) with an application image (HEX file generated by Nios® II SBT). The result of this combination is a (POF) which can be programmed to the flash using the Intel® Quartus® Prime Programmer.
In the Intel® Quartus® Prime software, "Convert Programming File tool" (quartus_cpf) can be called by selecting File >> Convert Programming Files.