Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers
The Computational Pan-Genomics Consortium (Consortium, 2016) described the role of coordinate systems in genomics as follows: “A pan-genome defines the space in which (pan-)genomic analyses take place. It should provide a ‘coordinate system’ to unambiguously identify genetic loci and (potentially nested) genetic variants.” The most natural representations of pangenomes are graphs. The Computational Pan-Genomics Consortium identified desirable properties of the linear reference genome model that graphical frameworks should attempt to preserve: spatiality, monotonicity, and readability. In this paper, we introduce a coordinate system for DAGs that has these properties. It is based on the level function and a minimum path cover of the graph. Moreover, we describe a new method for finding a minimum path cover in a DAG, which works very well in practice.
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- Büchler, Thomas
- Räther, Caroline
- Weber, Pascal
- Ohlebusch, Enno
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Category |
Paper in Conference Proceedings or in Workshop Proceedings (Paper) |
Event Title |
14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) |
Divisions |
Data Mining and Machine Learning |
Event Location |
Virtual |
Event Type |
Conference |
Event Dates |
11.-13.02.2021 |
Series Name |
Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS |
ISSN/ISBN |
978-989-758-490-9 |
Page Range |
pp. 21-29 |
Date |
11 February 2021 |
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