Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Fig 1
(A) Overview of the SALSA2 scaffolding algorithm. (B) Linkage information obtained from the alignment of Hi-C reads to the assembly. Arrows denote contigs and arcs between arrows denote the inferred linking information from Hi-C reads. Thickness of arcs denote the weight on the Hi-C edge. Thicker edge indicates higher edge weight implied by Hi-C reads (C) Assembly graph obtained from the assembler, where arrows are contigs and arcs denote overlap between contigs(D) Hybrid scaffold graph constructed from the links obtained from the Hi-C read alignments and the overlap graph. Solid edges indicate the linkages between different contigs and dotted edges indicate the links between the ends of the same contig. B and E denote the start and end of contigs, respectively. The E-E edge between blue and red contigs is dashed as this particular orientation between them is not supported by assembly graph, but rather B-E edge is supported. We ignore this dotted edge while computing maximal matching (E) Maximal weighted matching obtained from the graph using a greedy weighted maximum matching algorithm. The numbering of the edges indicates the order in which they were added to the graph. No more solid edges can be added to the matching as it would assign more than one edge to already matched nodes. (F) Edges between the ends of same contigs are added back to the matching to obtain final scaffolds.