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cs.DS2026
Computing Ultrabubbles in Linear Time by Reduction to Weak Superbubbles in the Double Covering Graph
Sebastian Schmidt, Juha Harviainen, Corentin Moumard +3
In recent years, in attempts to capture variation structures in genomic and pangenomic graphs, the zoo of bubbles has been filled with more and more different variants. The first m…
cs.DS2026
Identifying bubble-like subgraphs in linear-time via a unified SPQR-tree framework
Francisco Sena, Aleksandr Politov, Corentin Moumard +6
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph…
cs.DS2025
Identifying all snarls and superbubbles in linear-time, via a unified SPQR-tree framework
Francisco Sena, Aleksandr Politov, Corentin Moumard +4
Snarls and superbubbles are fundamental pangenome decompositions capturing variant sites. These bubble-like structures underpin key tasks in computational pangenomics, including st…