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

• Published in: iScience Vol. 26; no. 8; p. 107402
• Main Authors: Chao, Kuan-Hao, Chen, Pei-Wei, Seshia, Sanjit A., Langmead, Ben
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 18.08.2023; Elsevier
• Subjects: Algorithms; Bioinformatics; Data structure; Data structure; Bioinformatics; Algorithms
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2023.107402

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 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. [Display omitted] •Wheeler graphs are the basis of many pangenome and other sequence analysis tools•The WGT generates, recognizes, and visualizes Wheeler graphs•WGT’s Wheelie algorithm efficiently distinguishes Wheeler and non-Wheeler graphs•WGT’s bipartite Wheeler graph visualizer illustrates Wheeler graphs orderings Bioinformatics; Algorithms; Data structure