Duplex + UL assembly graph for Z. mays before manual resolution. In the maize assembly graph, most chromosomes are linear and resolved, except for regions of unresolved repeats (highlighted in red boxes), gaps on Chromosomes 1, 2, and 4, and the 45S rDNA array on Chromosome 6. ChrCP denotes the chloroplast and ChrMT denotes the mitochondria genomes, respectively. The callouts (A,B,C,D) correspond to low-coverage Duplex region, indicated by low coverage on the nodes. These regions were gap-filled using ONT UL sequences, generating additional noise in the graph. In each case, the path agreeing with the majority of ONT UL read alignments was selected for resolving the tangle. One end of Chromosome 3 was missing a telomere which was incorporated using ONT UL read consensus.
