After the sequencing with SOLiD, the original sequence of color coding will be accumulated. According to double-base coding matrix, the origi­nal color sequence can be decoded to get the base sequence if we knew the base types for one of any position in the sequence. Because of a kind of color corresponding four base pair, the color coding of the base will directly influence the decoding of its following base. It said that a wrong color coding will cause a chain decoding mistakes. BioScope is SOLiD data analysis package which provides a validated, single framework for resequencing, ChIP-Seq, and whole transcriptome analysis. It depends on reference for the follow-up data analysis. First, the software converts the base sequences of references into color coding sequence. Second, the col­or-coding sequence of references is compared with the original sequence of color-coding to get the information of mapping with newly developed mapping algorithm MaxMapper.