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These are represented as nodes with multiple incoming edges in the ARG.
A vertex with multiple incoming edges and, therefore, multiple parents, is constructed using substrings of all of the parent blocks.
Another modification of the model would be to use disjunctive instead of a conjunctive action of multiple incoming edges (Beerenwinkel et al., 2006).
In the ARG we define the following nodes: (a) the leaf nodes have no outgoing edges and they represent the extant unit (b) the coalescent nodes have single incoming edges, and (c) the exchange nodes have multiple incoming edges.
This progression is similar to the one proposed by the tree models of Jiang et al. (2000); yet the poset includes nodes with multiple incoming edges such as –Xp or –6q, which cannot be represented by a tree.
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In a de Bruijn graph, nodes having multiple incoming and outgoing edges can be divided into (i) those with two incoming edges and two outgoing edges and (ii) those with higher order connectivity (i.e. more than two incoming edges and more than two outgoing edges).
In a de Bruijn graph, in single-genome assembly, a node with multiple incoming and outgoing edges represents a repeat node.
A repeat node represents a sequence that occurs several times in the genome and can be described as a node at a crossing point between two paths with multiple incoming and outgoing edges.
We counted the number of nodes having multiple incoming and outgoing edges in de Bruijn graphs for both simulated data sets and real data sets of human gut microbial short read data.
Furthermore, we have applied splitting on incoming edges and addition of multiple incoming signals on a single target node.
Function assignment for different edge types is shown in Figure 2. Rules for multiple incoming and outgoing signals.
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