Fig. 3.

A Circos (Krzywinski et al., 2009) assembly consistency plot of conservative (a) ARCS (–c 5 –e 30000 –r 0.05 –l 5 –a 0.3) and (b) fragScaff (–C 5 –E 30000 –j 1 –u 4) scaffolding of the baseline scaffold assembly. Scaftigs from the largest 177 (ARCS) and 175 (fragScaff) scaffolds, consisting of 75% (N75) of the genome are aligned to GRCh38 with BWA mem. GRCh38 chromosomes are displayed incrementally from 1 (bottom, brown) to X (top, dark grey) on the left while scaffolds (black outlines) are displayed on the right side of the rim. Connections show aligned regions, 100 kbp and larger, between the genome and scaffolds. Large-scale misassemblies are visible as interrupting ribbons. The circles along chromosomes indicate centromeres, while the black regions on chromosomes indicate gaps in the reference