Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers

Thomas Büchler, Caroline Räther, Pascal Weber, Enno Ohlebusch

2021

Abstract

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.

Paper Citation

in Harvard Style

Büchler T., Räther C., Weber P. and Ohlebusch E. (2021). Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-490-9, SciTePress, pages 21-29. DOI: 10.5220/0010165400002865

in Bibtex Style

@conference{bioinformatics21,
author={Thomas Büchler and Caroline Räther and Pascal Weber and Enno Ohlebusch},
title={Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers},
booktitle={Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 3: BIOINFORMATICS},
year={2021},
pages={21-29},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0010165400002865},
isbn={978-989-758-490-9},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 3: BIOINFORMATICS
TI - Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers
SN - 978-989-758-490-9
AU - Büchler T.
AU - Räther C.
AU - Weber P.
AU - Ohlebusch E.
PY - 2021
SP - 21
EP - 29
DO - 10.5220/0010165400002865
PB - SciTePress