Table 3. Summary and metrics of MinION 2D read de novo assemblies before and after polishing.

	Number of contigs		Contig N50 (bps)		Max Contig size (bps)		Total contig size (bps)		Seq Identity %*
	Before polishing	After polishing	Before polishing	After polishing	Before polishing	After polishing	Before polishing	After polishing	Before polishing	After polishing
PBcR–Hybrid Assembly	22	13	616,079	673,428	2,033,791	2,384,872	5,499,815	5,499,838	>99.79%	>99.87%
PBcR–Non-hybrid Assembly	6	6	2,682,471	2,801,023	2,682,471	2,801,023	5,176,184	5,400,985	>93.71%	>98.55%
canu–Hybrid Assembly	15	13	1,378,273	1,688,510	1,690,109	1,690,462	5,490,339	5,491,108	>99.84%	>99.84%
canu–Non-hybrid Assembly	5	5	2,703,397	2,779,502	2,703,397	2,779,502	5,304,940	5,455,120	>95.45%	>97.94%
SPAdes–Hybrid Assembly	9	9	2,769,357	2,769,355	2,769,357	2,769,355	5,516,100	5,516,100	>99.96%	>99.97%

Number of contigs, contig N₅₀, largest contig length (“Max contig size”) and total contig lengths (“Total contig size”) are shown. Overall sequence identity percentages (“Seq Identity %”) to the reference Agrobacterium tumefaciens genome assembly before and after polishing are also shown, following alignments to the reference assembly with BLASTN. Only contigs >= 1 Kbps are listed; (*) Sequence identity percentages for contigs >= 10 Kbps only.