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- W4384276887 abstract "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." @default.
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- W4384276887 date "2023-08-01" @default.
- W4384276887 modified "2023-09-25" @default.
- W4384276887 title "WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs" @default.
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- W4384276887 doi "https://doi.org/10.1016/j.isci.2023.107402" @default.
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