What is the best way to interface ST7066 lcd controller with Atmel SAM4E
That controller, like many of its class, has an 8-bit and a 4-bit interface mode.  If you elect to use the 4-bit mode, you will use RS, R/W, E, DB4, DB5, DB6 and DB7 (7 pins total) to connect to the microprocessor.  If you use the 8-bit mode, it additionally uses DB0 through DB3 for a total of 11 pins. See the datasheet for details.

To further minimize the number of pins, you can wire RS and R/W low, but this means you can't read back from the controller.  Many simple projects that only use the built-in character generator can get away with this.

Typically, one uses GPIO pins for this kind of interface.