Dot plots of alignments of assemblies produced by minimus (top) and phrap (bottom) to the completed Brucella suis genome. The horizontal lines indicate the boundary between assembled contigs represented on the y axis. The vertical line separates between the two chromosomes of Brucella suis represented on the x axis. The minimus assembly (top) perfectly matches the reference sequence, as indicated by all matches lying along the main diagonal (except the contig at the bottom center, which spans the origin of the circular chromosome). The phrap assembly (bottom) shows many discrepancies with respect to the reference sequence (off-diagonal segments), including several contigs that incorrectly join segments of the two distinct chromosomes (e.g., second and third contigs from the bottom). Note that the ordering of the contigs implied by these figures is an artifact of the alignment to the reference sequence and does not correspond to the order in which the contigs were reported by the specific assembly tools. The discrepancies between the phrap assembly and the reference sequence prevent us from providing a consistent ordering for this assembly.