An example of a gap closed with two iterations of IMAGE in Plasmodium berghei. In the first iteration, IMAGE extended the contig consensus sequence from the right side of the gap, indicated by the green bar. In the second iteration, reads were aligned to the updated contig end. Local assembly of these reads along with their unaligned mates resulted in a new contig to completely close the gap, indicated by the red bar. The horizontal lines above the bars denote the Illumina reads realigned to the updated consensus sequence after each iteration. Below, a zoomed in plot shows the Illumina reads realigned against the closed gap.