Fig. 1

The Xander combined weighted assembly graph structure. M, I, and D represent HMM match, insert, and delete states, respectively. Numbers represent state position on the HMM. For simplicity, a kmer length of 6 is used and weights of the edges are not shown. The vertices shown in bold on the de Bruijn graph and profile hidden Markov model are combined to form the bold vertex in the combined graph. The green solid arrows represent all possible outgoing edges from these vertices. Boxes with ellipses indicate additional omitted graph structure. The delete HMM state is combined with the de Bruijn graph vertex from the last match; this carries forward the state information necessary to correctly form subsequent vertices in the combined graph. During path search, if this combined vertex becomes the best scoring vertex in the open set, it is removed from the open set and the adjacent combined vertices are instantiated and added to the open set