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arXiv · 2102.12824

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Sangsoo Park·Sung Gwan Park·Bastien Cazaux·Kunsoo Park·Eric Rivals
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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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Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, Eric Rivals. 2021-02-25. A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. https://arxiv.org/abs/2102.12824

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