Workflow of the SNP detection. All reads that were assembled and all reads that were marked as singletons but that can be mapped using ssaha2 (false positive singletons) served as input. Mapping of the reads and SNP detection was performed by three programs: Newbler, ssahaSNP, and bwa/SAMtools. For the latter two, the duplicates were removed using cd-hit-454. The workflow resulted in a set of SNPs, whereby those found by all tools are probable the most reliable SNPs.