How can I implement the DDR2 SDRAM or DDR3 SDRAM UniPHY PHY with my custom memory controller (instead of using the integrated Altera high-performance memory controller)?

The UniPHY-based memory interface IP cores are delivered with both the PHY and the controller integrated. In Quartus® II design software versions 10.0 SP1 and earlier versions, there is no MegaWizard option to instantiate the UniPHY PHY standalone for use with a custom controller. However, you can replace the Altera High-Performance memory controller with a custom memory controller by following the outlined procedure.

1. Parameterize and generate your variation of the UniPHY-based memory controller IP.
• This will generate a top-level HDL file called <variation_name>.v or .vhd, and a sub-directory named <variation_name> .
• The top-level module instanties the <variation_name>_controller_phy module. This module is located in the <variation_name>/ rtl directory and in-turn instantiates the PHY and controller.
• Controller module is named : <variation name>_alt_ddrx_controller
• PHY module is named : <variation name>_memphy_top
• The generated pin and timing constraint scripts require the design hierarchy to be maintained.
2. Open the <variation_name>/ rtl/<variation_name>_controller_phy.sv file. 
3. Replace the <variation name>_alt_ddrx_controller module with your custom controller module.
4. Delete the ports of the Altera High-Performance memory controller, and add the top-level ports of your custom controller.
5. Similarly, update the port names in top-level module in the <variation_name>.v or .vhd file.
6. Compile and simulate the design to ensure functionality.
7. Note that regenerating the UniPHY memory interface IP will erase all modifications made to the HDL files. And the parameters you select in the MegaWizard are stored in the top-level <variation_name> module. Hence, the steps above must be repeated everytime the IP variation is regenerated.