Now take the.sof file which you intended to program to the external SPI flash and convert that into a.flash file using Nios II command shell. #EPCS SERIAL FLASH CONTROLLER QSYS DOWNLOAD#
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Load the.sof file generated in step 2 on to the Altera FPGA. Generation of.sof (SRAM object) file for the Nios II project created in step 1. Creating a Nios II project (QSYS system which contains Nios II processor + EPCS flash controller). Here we describes an alternate method to program the SPI flashes which are not supported by the Quartus II Flash Programmer by using Altera’s Nios® II tool, which works with all versions of Quartus II software. There are some special cases in which altera programmer doesn’t work for third party SPI flash even after disabling the ID check while generating the.jic file. In such cases, users cannot use the built-in Quartus II Flash Programmer to program a JTAG Indirect File (*.jic) to the SPI flash, because the programmer checks the EPCS Device ID before initiating the programming. Altera recommends using their serial configuration devices (EPCS) in the Active Serial scheme, although users may prefer to use third party SPI flash instead of EPCS devices. In an Active Serial (AS) configuration scheme, a SPI flash device can be used to configure the Altera FPGA that acts as the configuration master while the SPI flash acts as a slave. 
Therefore select 'Library >Memories and Memory Controllers >External Memory Interfaces >Flash Interfaces >EPCS Serial Flash Controller'. In the example project, this is the file epcq_controller.hex. The hex file with the same name as the Altera Serial Flash Controller QSys instance is the file needed to create the.jic file.
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