Gerber Files

Gerber files are generated by software tools that were used to design a pcb.

these files are sent to the pcb manufacture to produce the pcb.

quartus is used as a tool to generate files that decrive the behavioral of an altera device that is mounted on such a pcb.

the only point where both worlds, the gerber and altera, are getting in contact via a schematic entry as a top level or pcb direct entry (but who would do that with up to 1000 pads?). to define the connection between signals on the pcb and the altera device.

pcb design tools, like altium designer, handle such an interface automatically with pinswapping and fpga device or manufacture swapping automatically.