Which application is used to burn BOOT.bin on a brand new QSPI flash (with JTAG programmer)?

In Zynq UltraScale+ RFSoC SOM (ZU49/ZU48DR), Vitis 2022.2 tool is used to program the QSPI on a new board. Please refer section “Programming QSPI” from software user guide for more information.

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Please find the detailed product information here:
ZU49/ZU39/ZU29DR RFSoC System on Module

ZU48/47/43/28/27/25DR RFSoC System on Module