Basically, this color error means that C's become A's and A's become C's. Likewise for G's and T's. For the three different types of errors, we get three different ends of the read. Along with the correct reads, we may get four different versions of the original genome due to errors. So if SOLiD reads are just regarded in nucleotide space, we get four different contig sequences with jumps from one to another every time there is a sequencing error.
Thus, to fully accommodate SOLiD sequencing data, the special nature of the technology has to be considered in every step of the assembly algorithm. Furthermore, SOLiD reads are fairly short and often quite error prone. Due to these issues, we have chosen not to include SOLiD support in the first algorithm steps, but only use the SOLiD data where they have a large positive effect on the assembly process: when applying paired information.