Figure 3.

Canu GFA output localizes complex repeat regions, allowing for improved scaffolding. (A) Bandage (Wick et al. 2015) plot of D. melanogaster compared with the karyotype (Stevens 1912; Metz 1914) from FlyBase (Attrill et al. 2016). Nodes are contigs sized by length, and edges indicate unused overlaps between contigs. The largest contigs are colored randomly and labeled with their chromosome based on alignment to the reference. (B) The callout shows Chromosome 2L from positions 3.07–23.12 Mbp, redrawn with the centromere at the top (indicated by a filled circle). Unique contigs are shaded black, while repeat contigs are shaded red. While the 2L chromosome scaffold is composed of 10 individual contigs, they are all linked in the output graph. The two red regions correspond to reference gaps at positions 2L:21,485,538, which consist of 100–200 copies of the histone gene cluster spanning >500 kbp and 2L:22,420,241, which is bordered by several TE repeats (Hoskins et al. 2015). The break in the bottom left of Chromosome 2L could not be confidently identified but is next to a feature labeled “FlyBase transposable element” in the genome annotation and is likely a transposable element insertion site. Even though Canu is unable to fully resolve these large repeat arrays, the graph indicates large-scale continuity across Chromosome 2L and could enable resolution with secondary technologies.