Fig. 1
From: Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
An overview of the CUTTLEFISH 2 algorithm. It is capable of constructing the compacted de Bruijn graph from a collection of either reference sequences or raw sequencing reads. The edges ((k+1)-mers) of the underlying de Bruijn graph are enumerated from the input, and optionally filtered based on the user-defined threshold. The edges are then used to enumerate the vertices (k-mer) they contain. An MPHF is constructed over the set of vertices, to associate the DFA-state of each vertex to it. Then the edge set is iterated over to determine the state of the DFA of each vertex in the graph, by transitioning the DFA through appropriate states, based on the edges in which the vertex is observed. Then an iteration over the original vertices to stitch together appropriate edges allows the extraction of the maximal unitigs