Plasmid Reconstruction and Validation

Explain plasmid modular organisation and the limitations of replicon-based plasmid classification.

Run MOB-recon and inspect its evidence to separate candidate plasmid sequences from chromosomal sequence.

Distinguish autonomous plasmids from chromosomal integrations and unresolved repeat-linked contigs.

Run MOB-typer and PlasmidFinder to characterise plasmid replicons, relaxases, mating systems, oriT signals, and predicted mobility.

Run ISEScan and IntegronFinder and use curated similarity searches to annotate insertion sequences, transposons, and integrons around carbapenemase genes.

Diagnose plasmid reconstruction ambiguity caused by repeats, cointegrates, or multiple related plasmids.