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Is it USB, PCIe, or something else? I ask because I'm looking for a way to read/write the hidden boot1 and boot2 partitions on an eMMC chip, and it just doesn't work over USB.

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Unsurprisingly, the bus supporting SD cards is called SD bus. There is a spec for it if you're interested. The SoC of RPi 3 implements two controllers for this bus: one is connected to the microSD slot, and the other one to the WiFi controller in SDIO mode.

The Linux driver for SD/MMC/SDIO devices is called mmc, and it does provide access to the hidden partitions. To use the SD slot, you will need to boot from something else than the SD card.

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