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Graph links
Isaac Turner edited this page Mar 3, 2016
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Links are paths through a graph (de bruijn or unitig) -- we focus on de bruijn graph. Links are added to kmers to connect them to other kmers. This helps resolve areas of low complexity in the graph. Links are created from reads with the thread command. Links help us assemble longer contigs when traversing the graph.
- Link information will always occur on a kmer immediately preceding a junction (i.e. in-degree greater than one)
- Orientation of link (forward (F) or reverse (R)) is w.r.t. 'kmer-key' (the lexically lower of a kmer and its reverse complement)
- If a link starts at kmer A and ends at kmer B, there exists a link on kmer B that goes from B to A
Rule 1 may also be re-written in terms of unitigs as:
Link information may only occur on the first node of a supernode going in the opposite direction, or the last node going in the same direction. When a unitig is only one node long this means the node may have links going in both directions.
Given three points in a graph: A,B,C, if we can traverse from B->A and from A->C, then we can traverse from B->C.