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WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs

View ORCID ProfileKuan-Hao Chao, Pei-Wei Chen, Sanjit A. Seshia, View ORCID ProfileBen Langmead
doi: https://doi.org/10.1101/2022.10.15.512390
Kuan-Hao Chao
1Department of Computer Science, Johns Hopkins University
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  • For correspondence: kh.chao@cs.jhu.edu langmea@cs.jhu.edu
Pei-Wei Chen
2Department of Electrical Engineering and Computer Sciences, University of California, Berkeley
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Sanjit A. Seshia
2Department of Electrical Engineering and Computer Sciences, University of California, Berkeley
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Ben Langmead
1Department of Computer Science, Johns Hopkins University
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  • For correspondence: kh.chao@cs.jhu.edu langmea@cs.jhu.edu
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Abstract

Summary A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome indexes. However, there are no practical tools to visualize or to check graphs that may have the Wheeler properties. Here we present Wheelie, an algorithm that combines a renaming heuristic with a Satisfiability Modulo Theory (SMT) solver to check whether a given graph has the Wheeler properties, a problem that is NP complete in general. Wheelie can check a variety of random and real-world graphs in far less time than any algorithm proposed to date. It can check a graph with 1,000s of nodes in seconds. We implement these algorithms together with complementary visualization tools in the WGT toolkit, available as open source software at https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • I fixed two reference links in the appendix file

  • https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 21, 2022.
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WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
Kuan-Hao Chao, Pei-Wei Chen, Sanjit A. Seshia, Ben Langmead
bioRxiv 2022.10.15.512390; doi: https://doi.org/10.1101/2022.10.15.512390
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WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
Kuan-Hao Chao, Pei-Wei Chen, Sanjit A. Seshia, Ben Langmead
bioRxiv 2022.10.15.512390; doi: https://doi.org/10.1101/2022.10.15.512390

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