Figure 1.

CONTIGuator. a) Program flowchart: the input contigs are mapped to the reference using the combination of Blast and MUMmer, generating a map (viewable with ACT), Primer3 provides a series of PCR primers that can be used to generate a new set of contigs, from which the process can be iterated again; b-c-d-e) ACT visualization: the reference genome is on top, pseudocontig on bottom; b) a putative primer placement over two near contigs; c) a section of no synteny in an otherwise fully syntenic contig; d) a region of the reference genome with no homolog in the mapped contig; e) the same region in d) highlighted, since it harbors a tblastn hit against the excluded contigs; f-g) verification of structural clues in ACT: the closed genome of Sinorhizobium meliloti BL225C is on top, the reference genome in the middle and the contigs on bottom.