Table 3. The total number of plasmids recovered by each tool; there were 59 total reference plasmids in the 30 samples.

Tool	Complete plasmids recovered	Total plasmids partially recovered or misassembled	Total plasmids missed	Additional plasmids recovered not in reference	Samples with additional non-plasmid contigs recovered
Hybracter hybrid	65	4	0	2	10
Unicycler	60	6	3	1	2
Dragonflye hybrid	44	16	9	1	10
Hybracter long	60	5	4	2	3
Dragonflye long	44	16	9	1	10