Fig. 1

Flow chart of the Haploflow algorithm and its two parts: First, the construction of the deBruijn graph and operations thereon, namely splitting it by connected components and calculating coverages. Then, the creation of the unitig graphs per CC and the assembly process consisting of calculating the thresholds and the coverage histograms and the putative paths through the graphs. Next is the calculation of the concrete flows and thereby the generation of the contigs and finally the cleaning of the graph and the generation of the assembly graphs. As intermediate output, the assembly graph is created during every step (bottom left)