Table 2.

Number of unique contigs by sequencing modality and bacterial species. Using the complete data available (i.e. no subsampling). The first number in each cell represents the number of contigs assembled and matching to the Illumina-corrected reference using dnadiff, the total number of contigs assembled is shown in curved brackets, and the proportion of the reference chromosomal contig covered in square brackets. For E. coli , P. aeruginosa , S. aureus the total number of expected contigs is one, for K. pneumoniae one chromosome +5 plasmids. Orange shading shows absent contigs, and/or incomplete assembly (n>1 contig matching to reference), and/or extra contigs not matching to reference. Green shaded cells denote complete singular contigs which reflect the reference DNA content at 100+/-1 %. “-“ denotes no relevant contig assembled

Sequencing modality	Assembler	Plexed Y/N	E. coli , chromosome [1] 5 231 428 bp 51 % GC	P. aeruginosa , chromosome [1] 6 264 404 bp 66.2%GC	S. aureus , chromosome [1] 2 902 619 bp 32.8%GC	K. pneumoniae , chromosome [1] 5 315 120 bp 57.0%GC	K. pneumoniae , pKPN3 plasmid [1] 1 75 879 51.7%GC	K. pneumoniae , pKPN4 plasmid [1] 1 07 576 bp 53.4%GC	K. pneumoniae , pKPN5 (plasmid [1] 88 582 bp 53.8%GC	K. pneumoniae , pKPN6 (plasmid [1] 4259 bp 41.4%GC	K. pneumoniae , pKPN7 (plasmid [1] 3478 bp 45.7%GC
Illumina	SPAdes	Y	226 (326) [98.64 %]	115 (152) [99.72 %]	86 (150) [98.42 %]	117 (312) [98.9 %]	41 [79.7 %]	45 [100.72 %]	22 [82.49 %]	1 [102.82 %]	1 [103.45 %]
R9.4.1 hac +Illumina	Unicycler	Y	1 [1] [100.09 %]	1 [1] [100.49 %]	1 [1] [100.69 %]	1 [7] [100.1 %]	1 [100 %]	1 [100 %]	1 [100 %]	2 [100 %]	1 [96.15 %]
R9.4.1 hac	Canu	Y	1 [1] [100.59 %]	1 [1] [101.29 %]	1 [1] [103.18 %]	1 (24) [100.72%]	1 [131.55 %]	1 [172.51 %]	1 [100 %]	2 [133.5 %]	1 [100 %]
R9.4.1 sup	Canu	Y	1 [1] [100.65 %]	1 [1] [101.18 %]	1 [1] [102.43 %]	1 [7] [100.96%]	1 [129.41 %]	1 [100 %]	1 [125.07 %]	1 [100 %]	1 [100 %]
R10.3 hac	Canu	N	1 [6] [100.49 %]	1 [2] [101.19 %]	1 [3] [102.78 %]	1 [8] [100.72 %]	1 [100 %]	1 [100 %]	1 [100 %]	1 [100 %]	1 [100 %]
R10.3 sup	Canu	N	1 [2] [100.6 %]	1 [3] [101.13 %]	1 [3] [102.85]	1 [8] [100.74 %]	1 [100 %]	1 [138.13 %]	1 [143.94 %]	1 [192.58 %]	1 [100 %]
R10.4 hac	Canu	N	1 [6] [100.62 %]	1 [1] [101.06 %]	1 [2] [103.6 %]	1 [8] [100.8 %]	1 [127.89 %]	1 [141.81 %]	1 [147.6 %]	1 [100 %]	1 [112.85 %]
R10.4 sup	Canu	N	1 [3] [100.61 %]	1 [2] [100.1 %]	1 [2] [102.33 %]	1 [7] [100 %]	1 [100.94 %]	1 [100 %]	1 [145.43 %]	1 [100 %]	1 [100 %]
R10.4 sup duplex	Canu	N	4 (42) [100.12 %]	1 [14] [101.5 %]	1 (29) [101.72%]	1 (41) [100.1 %]	1 [100 %]	3 [130.98 %]	1 [149.19 %]	1 [100 %]	1 [100 %]
R10.4 hac	Canu	Y	1 [2] [100.42 %]	1 [1] [100.87 %]	1 [1] [102.01 %]	1 [7] [100.82 %]	1 [124.01 %]	1[100 %]	1 [142.89 %]	1 [100 %]	1 [100 %]
R10.4 sup	Canu	Y	1 [1] [100.48 %]	1 [1] [100.17 %]	1 [1] [102.29 %]	1 [12] [100.61 %]	1 [117.3 %]	2 [134.06 %]	1 [137.68 %]	1 [100 %]	1 [100 %]
R10.4 sup duplex	Canu	Y	-*	23 (25) [99.2 %]	-*	15 (25) [99.2 %]	1 [80.39 %]	2 [97.73 %]	1 [112.86 %]	1 [94.01 %]	1 [100 %]
R9.4.1 hac	Flye	Y	1 [1] [100.09 %]	1 [1] [100.14 %]	1 [1] [100.7 %]	1 [4] [100.11 %]	1 [75.7 %]	1 [103.68 %]	1 [100 %]	–	–
R9.4.1 sup	Flye	Y	1 [1] [100.09 %]	1 [1] [100.47 %]	1 [1] [100 %]	1 [5] [100.1 %]	1 [100 %]	1 [99.99 %]	1 [100 %]	–	–
R10.3 hac	Flye	N	1 [1] [100.10 %]	1 [1] [100.44 %]	1 [1] [100.69 %]	1 [4] [100.1 %]	1 [95.83 %]	1 [73.13 %]	1 [100 %]	–	–
R10.3 sup	Flye	N	1 [1] [100.09 %]	1 [1] [100.44 %]	1 [1] [100.69 %]	1 [4] [100.1 %]	1 [100 %]	1 [100 %]	1 [100 %]	–	–
R10.4 hac	Flye	N	1 [1] [100.10 %]	1 [1] [100.11 %]	1 [1] [100.69 %]	1 [4] [100.1 %]	1 [100 %]	1 [100 %]	1 [100 %]	–	–
R10.4 sup	Flye	N	1 [1] [100.09 %]	1 [1] [100.4 %]	1 [1] [100.69 %]	1 [5] [100.1 %]	1 [100 %]	1 [98.92 %]	1 [99.99 %]	–	–
R10.4 sup duplex	Flye	N	1 [3] [100.10 %]	1 [1] [100.8 %]	1 [2] [100.69 %]	1 [7] [100.21 %]	1 [94.27 %]	1 [102.93 %]	1 [101.54 %]	–	1[100 %]
R10.4 hac	Flye	Y	1 [1] [100.10 %]	1 [1] [100.16 %]	1 [1] [100.69 %]	1 [5] [100.1 %]	1 [100 %]	1 [100 %]	1 [100 %]	–	–
R10.4 sup	Flye	Y	1 [1] [100.00 %]	1 [1] [100.48 %]	1 [1] [100.69 %]	1 [5] [100.11 %]	1 [100 %]	1 [100 %]	1 [100 %]	–	–
R10.4 sup duplex	Flye	Y	37(38) [8.47 %]	1 [5] [100.48 %]	25(25) [83.64 %]	1 [4] [100.4 %]	1 [84.71 %]	1 [105.27 %]	1 [100 %]	–	–

^*Insufficient read depth for canu to assemble using default settings.