Figure 2
The same example as in Figure 1, but in this example, the assembly algorithm honors SNP positions that were detected during earlier iterations of the assembly process. The alignment between s1 and s2 will, therefore, not be made, as there is a mismatch at the SNP position, even with the long overlap between both sequences. Instead, the assembler will align s1 and s1*, as they do not contain mismatches at SNP positions. The result is a correct representation of the transcriptome.
