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

Explain the evidence MOB-recon uses to classify plasmid and chromosomal sequences before running and checking its commands.

Discriminate between a one-copy Unicycler assembly and a three-copy Autocycler carbapenemase locus by comparing short-read BWA-MEM and samtools depth evidence before testing long-read spanning and repeat-junction support.

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

Explain replicons, relaxases, mating systems, oriT sites, and predicted mobility before running MOB-typer and PlasmidFinder.

Explain insertion sequences, transposons, and integrons before running ISEScan, IntegronFinder, and curated searches around carbapenemase genes.

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