RT Journal Article
SR Electronic
T1 WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.10.15.512390
DO 10.1101/2022.10.15.512390
A1 Chao, Kuan-Hao
A1 Chen, Pei-Wei
A1 Seshia, Sanjit A.
A1 Langmead, Ben
YR 2022
UL http://biorxiv.org/content/early/2022/10/21/2022.10.15.512390.abstract
AB 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 StatementThe authors have declared no competing interest.