The read graph G = (V, E) is a directed graph with vertices corresponding to reads aligned with the consensus sequence. For a read u, we denote by b(u), respectively e(u), the genomic coordinate at which the first, respectively the last, base of u gets aligned. A directed edge (u, v) connects read u to read v if a suffix of u overlaps with a prefix of v and they coincide across the overlap. Two auxiliary vertices -a source s and a sink t are added such that s has edges into all reads with zero indegree and t has edges from all reads with zero outdegree. Then each st-path corresponds to a possible candidate quasispecies sequence. The read graph is transitively reduced, i.e., each edge e = (u, v) is removed if there is a uv-path not including edge e. Note that certain reads can be completely contained inside other reads. Let a superread refer to a read that is not contained in any other read and let the rest of the reads be called subreads. Subreads are not used in the construction of the read graph, but are taken into account in the final assembly of candidate sequences and frequency estimation.