I am not sure, in terms of sequencing what is referred to as color space and nucleotide space. What is a difference between a normal reference genome and a color space genome. Does it has to do something with base calling, that the original data is retained without the conversions to textual nucleotide data!!!! What we use in normal chip-seq and rna-seq analysis.
There's a kind of similar question here but the answer is missing the link.