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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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A Multi-flow Approach for Binning Circular Plasmids from Short-Reads Assembly Graphs

  • 会议论文

  • 发表日期：

    2026年

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  • Victor Epain,
  • Aniket Mane,
  • Gianluca Della Vedova,
  • Paola Bonizzoni,
  • Cedric Chauve

摘要

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.