Figure 3.

Visualization of REAPR output after analysing a de novo assembly. The results of running on the GAGE S. aureus Velvet assembly are shown (partly displayed using Circos [36]). Similarity by BLAST between the reference (grey) and the assembly (blue) is marked with blue bands. Only the BLAST hits to the largest scaffold from the assembly are shown, representing approximately 30% of the genome. One megabase of reference sequence that does not match the assembly supercontig of interest has been removed. The top plot shows the score output from REAPR, with the highest values corresponding to error-free bases. Error calls are marked with blue circles. The second plot shows the FCD error, with peaks corresponding to the error calls and low score regions. Next, heatmaps of the type of read coverage are shown for the forward and reverse strand: proper read pairs (red), orphaned reads (green), reads mapped too close or too far apart (blue) and reads oriented incorrectly (purple). The bottom plot shows the fragment coverage. (a, b) show zoomed in regions of the figure. (a) A deletion from the assembly, where the score drops, the FCD error increases and most reads flanking the deletion are orphaned. (b) A region of the assembly containing many repeats.