We address the problem of plasmid binning, that aims to group contigs—from a draft short-read assembly for a bacterial sample—into bins each expected to correspond to a plasmid present in the sequenced bacterial genome. We formulate the plasmid binning problem as a network multi-flow problem in the assembly graph and describe a Mixed-Integer Linear Program to solve it. We compare our new method, PlasBin-HMF, with state-of-the-art methods, MOB-recon, gplasCC, and PlasBin-flow, on a dataset of more than 500 bacterial samples, and show that PlasBin-HMF outperforms the other methods, by preserving the explainability.
Epain, V., Mane, A., Vedova, G., Bonizzoni, P., Chauve, C. (2026). A Multi-flow Approach for Binning Circular Plasmids from Short-Reads Assembly Graphs. In Comparative Genomics 23rd RECOMB International Workshop, RECOMB-CG 2026, Thessaloniki, Greece, May 24–25, 2026, Proceedings (pp.91-105). Springer Science and Business Media Deutschland GmbH [10.1007/978-3-032-26891-4_5].
A Multi-flow Approach for Binning Circular Plasmids from Short-Reads Assembly Graphs
Vedova G. D.;Bonizzoni P.;
2026
Abstract
We address the problem of plasmid binning, that aims to group contigs—from a draft short-read assembly for a bacterial sample—into bins each expected to correspond to a plasmid present in the sequenced bacterial genome. We formulate the plasmid binning problem as a network multi-flow problem in the assembly graph and describe a Mixed-Integer Linear Program to solve it. We compare our new method, PlasBin-HMF, with state-of-the-art methods, MOB-recon, gplasCC, and PlasBin-flow, on a dataset of more than 500 bacterial samples, and show that PlasBin-HMF outperforms the other methods, by preserving the explainability.
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