Table 1.
Plasmid sequences inferred from the Nanopore and/or Illumina sequencing assemblies of pure plasmid DNA or of total genomic DNA.
| Strain | Plasmid Size (kb) a | Nanopore- Only b Contig (bp) |
Nanopore- Polished c Contig (bp) |
Illumina-Only d Contig (bp) |
Illumina-Hybrid e Contig (bp) |
|---|---|---|---|---|---|
| Pure Plasmid DNA | |||||
| E. coli DU1040 (NR1) | 94.289 | Several contigs f | 93,868 | Several contigs | 94,308 |
| K. pneumoniae | 232 | 313,736 | 313,014 | Several contigs | Several |
| LST1504-C2 | 153 | 265,010 | 265,397 | Several contigs | Several |
| 71 | 58,149 | 58,214 | Several contigs | Several | |
| 6 | 3380 | 3378 | 3003 | 6261 | |
| E. ludwigii LST1391B | 158.6 | 133,397 | 133,378 | 130,070 | 130,070 |
| 7 | 5187 | 5152 | 5283 | 5152 | |
| Total Genomic DNA | |||||
| E. coli DU1040 (NR1) | 94.289 | 94,296 | 94,410 | Several contigs | 93,656 |
| K. pneumoniae | 232 | 313,645 | 312,971 | Several contigs | 314,384 |
| LST1504-C2 | 153 | 264,823 | 264,679 | Several contigs | Several |
| 71 | 58,157 | 58,118 | Several contigs | Several | |
| 6 | 3350 | 3326 | 2930 | 2930 | |
| E. ludwigii LST1391B | 158.6 | 133,990 | 133,333 | 130,070 | 130,070 |
| 7 | 6174 | 6174 | Several contigs | 5033 | |
a Plasmid sizes were roughly estimated using standard electrophoresis. b Nanopore-only: MinION reads were assembled using Flye, without error correction of lllumina reads. c Nanopore-polished: MinION reads were assembled using Flye and polished with Illumina reads. d Illumina-only: Illumina reads were assembled using SPADES, without error correction with Nanopore reads. e Illumina-hybrid: assembly of Illumina reads and Nanopore reads with hybridSPADES, polished with Illumina reads. f Several: two or more contigs of different lengths matched with the control or with a plasmid sequence from GenBank.