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Optimal Construction of Hierarchical Overlap Graphs

Author Shahbaz Khan

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Author Details

Shahbaz Khan
  • University of Helsinki, Finland

Funding

This work was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851093, SAFEBIO).

Acknowledgements

I would like to thank Alexandru I. Tomescu for helpful discussions, and for critical review and insightful suggestions which helped me in refining the paper. I would also like to thank Veli Mäkinen for pointing out the similarity with the classical result for APSP problem.

Cite As Get BibTex

Shahbaz Khan. Optimal Construction of Hierarchical Overlap Graphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 17:1-17:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021) https://doi.org/10.4230/LIPIcs.CPM.2021.17

Abstract

Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such as de Bruijn graphs or overlap graphs, which maintain partial information about such overlaps. For genome assembly algorithms, these graphs present a trade-off between overlap information stored and scalability. Thus, Hierarchical Overlap Graph (HOG) was proposed to overcome the limitations of both these approaches.
For a given set P of n strings, the first algorithm to compute HOG was given by Cazaux and Rivals [IPL20] requiring O(||P||+n²) time using superlinear space, where ||P|| is the cumulative sum of the lengths of strings in P. This was improved by Park et al. [SPIRE20] to O(||P||log n) time and O(||P||) space using segment trees, and further to O(||P||(log n)/(log log n)) for the word RAM model. Both these results described an open problem to compute HOG in optimal O(||P||) time and space. In this paper, we achieve the desired optimal bounds by presenting a simple algorithm that does not use any complex data structures. At its core, our solution improves the classical result [IPL92] for a special case of the All Pairs Suffix Prefix (APSP) problem from O(||P||+n²) time to optimal O(||P||) time, which may be of independent interest.

Subject Classification

ACM Subject Classification
  • Mathematics of computing → Trees
  • Theory of computation → Data compression
  • Theory of computation → Pattern matching
Keywords
  • Hierarchical Overlap Graphs
  • String algorithms
  • Genome assembly

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