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2.5. Programming with Flash Loaders
Parallel and serial configuration devices do not support the JTAG programming interface. However, you can use a flash loader to program configuration devices in-system via the JTAG interface. The flash loader allows an FPGA to function as a bridge between the JTAG interface and the configuration device. The Intel® Quartus® Prime software supports various parallel and serial flash loaders for programming bitstream storage and configuration via flash memory devices.
Refer to the following documents for step-by-step flash programming instructions.