Do I need an external PHY when using the Altera SoC's USB controller?

SoC FPGAs

Yes.

Please refer to the configuration from the public document (URL below) of the Altera development kit with the SoC device mounted.

Cyclone V SoC Development Kit
  https://www.altera.co.jp/products/boards_and_kits/dev-kits/altera/kit-cyclone-v-soc.html


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