The assembly graph------------------|Orgasm| rely on a graph representation of the ongoing assembly. The graph used is what iscalled a `De Bruijn graph <https://en.wikipedia.org/wiki/De_Bruijn_graph>`_ but restricted to nodes representing substrings of a given length of the genome to reconstruct. .. figure:: ./graph.* :align: center :figwidth: 80 % :width: 500 An example of the underlying graph (adapted from `Compeau et al. (2011) <http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html>`_)In our particular case, we work with words of the length of the reads produced by the shotgunsequencing. So the graph is also what is called a string graph for our set of reads (see`Meyers (2005) <http://bioinformatics.oxfordjournals.org/content/21/suppl_2/ii79.abstract>`_for details).