Epain, V.; Mane, A.; Della Vedova, G.; Bonizzoni, P.; Chauve, C.

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.