Hi-C contact frequency files - which genome to use?

[aminakur]

Hi, thank you for developing the tool. I am confused as to which reference genome is being used when generating Hi-C contact frequency files of each species (to be stored in path_list.txt file).
"The normalized Hi-C contact frequency file on a chromosome could be extracted from the raw genome-wide Hi-C contact frequency file of the species using tools such as the Juicer Tools."
Here, the .hic file to use for extracting the Hi-C contact frequency - is it generated using the reference genome when aligning the Hi-C sequencing reads, or is it a file of the species the reads were generated from (non-reference)?