Fig. 4
From: EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends
a Construction and cleaning of the scaffolding graph. Each contig have two nodes representing the left contig end and the right contig end. The two nodes from the same contig were tied together and won’t be broken, and the two nodes from different contigs if the corresponding contact value is larger than a specified cutoff, were assigned an edge. Branching edges that do not satisfy the reciprocal best requirement will be excluded, and circular paths are broken at the position with lowest contact value. b Rules for determining relative contig order and orientation by the reliable links (edge) between neighbor contig ends. The color green and blue indicate contig and contig end, respectively. The connecting line indicate reliable link between adjacent contig ends. The mark “+” and “−” means forward and reverse strands assigned in the GFA file. c Example graphic view (Bandage) of cleaned scaffolding graph with contig end size 1.5 Mb and contact cutoff of 1.5 times of the turning point for great burdock, 28 large contigs were linked into 18 linear paths (anchor rate > 99%), with each path corresponding to a natural chromosome. Small clusters with length less than 1 Mb are not shown. Using raw and normalized matrix data generates the same result