Fig. 6.

Four dot plots of scaffolds along human chromosome 8. The top row shows dot plots where the reference genome is on the x-axis and scaffolds output by 3D-DNA (left) and HiC-Hiker (right) are on the y-axis. The red-colored dots indicate correct orientations of contigs (forward alignment with the reference) while the blue-colored dots show erroneous orientations (reverse-complement alignments). The dot plots show that the reference is mostly covered by contigs. The total length of contigs in the scaffolds is 123 011 808 bp, which is close to 145 138 636 bp, i.e. the length of chromosome 8 in hg38. In the left bottom portions of both of the upper dot plots, we see large reverse-complement alignments of the reference and scaffolds. In the lower dot plots, we enlarged parts of the upper two plots to show the reference genomic region, which ranges from 65 to 74 Mb. The six orientation errors of short contigs shown in the lower left plot shown as blue dots are corrected in the HiC-Hiker scaffold shown in the lower right plot