A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs
Abstract
The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P || log n) time and O(||P ||) space, where ||P || is the sum of lengths of the strings in P. In this paper we present a new algorithm to construct HOG in O(||P ||) time and space. Hence, the construction time and space of HOG are better than those of the overlap graph, which are O(||P || + n 2).
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