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bioRxiv · 10.1101/2022.10.15.512390

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

Chao, K.-H.·Chen, P.-W.·Seshia, S. A.·Langmead, B.
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Abstract

SummaryA 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 permutation solver (Wheelie-PR) or a Satisfiability Modulo Theory (SMT) solver (Wheelie-SMT) 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.

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Chao, K.-H., Chen, P.-W., Seshia, S. A., Langmead, B.. 2022-10-18. WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs. https://doi.org/10.1101/2022.10.15.512390

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