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Can AT90USBKEY be used as dev. board for USB host device?

What I would like to try is to use this board to check if I can send SCPI commands to some third party device via USB.

And can this usb miniAB from this dev. board be used to connect to usb type B on that third party device, and if not, how else this communication can be achieved?

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According to the user guide, p9:

When connected to a mini B plug, the AT90USB operates as an “USB device” (the ID pin of the plug is unconnected) and when connected to a mini A plug, the AT90USB operates as a “USB host” (the ID pin of the A plug is tied to ground).

So yes, the board can operate in host mode so long as you use a USB-OTG cable to ensure correct setting of the ID pin.

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