Closing gaps in de novo assembly comprising only Illumina reads. Schematic diagram showing the comparison of the original velvet assembly (3 contigs a, b and c) and the improved assembly in Salmonella enterica. The improved assembly was aligned to the reference sequence with 99.8% identity. The two closed gaps shown were 100% identical to the reference sequence. Contigs are indicated by grey bars; gene annotations are indicated by yellow boxes. Vertical lines highlight the gaps that are filled by IMAGE in the improved contigs. Below, a coverage plot showing the relatively even depth of coverage of realigned Illumina reads at the improved assembly, indicating no signature of misassembly.