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bioRxiv · 10.64898/2026.03.25.714305

A multi-flow approach for binning circular plasmids from short-reads assembly graphs

Epain, V.·Mane, A.·Della Vedova, G.·Bonizzoni, P.·Chauve, C.
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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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Epain, V., Mane, A., Della Vedova, G., Bonizzoni, P., Chauve, C.. 2026-03-26. A multi-flow approach for binning circular plasmids from short-reads assembly graphs. https://doi.org/10.64898/2026.03.25.714305

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