Abstract
The problem of analysing bacterial isolates in order to detect plasmids has been widely studied. With the development of Whole Genome Sequencing (WGS) technologies, several approaches have been proposed to bin contigs into putative plasmids. Reference-based approaches aim to bin contigs by mapping or comparing their sequences against databases of previously identified plasmids or plasmid genes. On the other hand, de novo approaches use contig features such as read coverage and length for plasmid binning. Hybrid approaches that combine both strategies have also been proposed recently.
We present PlasBin a mixed integer linear programming based hybrid approach for plasmid binning. We evaluate the performance of several binning methods on a real data set of bacterial samples.
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Notes
- 1.
We rely on Unicycler as it is a widely used bacterial genome assembler, but any assembler providing an assembly graph can be used.
- 2.
Our data set did not contain any samples from Acinetobacter baumannii.
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Mane, A., Faizrahnemoon, M., Chauve, C. (2022). A Mixed Integer Linear Programming Algorithm for Plasmid Binning. In: Jin, L., Durand, D. (eds) Comparative Genomics. RECOMB-CG 2022. Lecture Notes in Computer Science(), vol 13234. Springer, Cham. https://doi.org/10.1007/978-3-031-06220-9_16
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