Table 2.
MicroPIPE v0.9 results for public datasets
| Reference | Strain | Reference genome assembly method and coverage | Chromosome/plasmid | Reference genome size (bps) | Assembly size (bps) | GC content (%) | Circular? | Nucleotide Identity (%) | DNAdiff SNPs GSNPs |
DNAdiff Indels | QUAST misassemblies |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Clement et al. [51] | Salmonella enterica serovar Napoli strain LC0541/17 | Canu using Nanopore + Illumina 37x |
Chromosome pLC0541_17 |
4,679,033 90,558 |
4,679,747 90,578 |
52.2 |
Yes Yes |
99.97 |
510 390 |
758 | 0 |
| Sydenham et al. [52] | Bacteroides fragilis strain DCMOUH0042B (BF042) | Unicycler using Nanopore + Illumina 200x |
Chromosome pBFO42_1 pBFO42_2 |
5,141,257 8306 5594 |
5,141,261 8316 5629 |
43.3 |
Yes Yes Yes |
99.99 |
65 9 |
14 | 0 |
| Sydenham et al. [52] | Bacteroides fragilis strain CCUG4856T | Unicycler using Nanopore + Illumina 200x |
Chromosome pBF9343 |
5,205,133 36,560 |
5,205,138 36,559 |
43.1 |
Yes Yes |
99.99 |
25 5 |
22 | 1 (inversion) |
| Walker et al. [53] | Streptococcus pyogenes strain SP1336 | Pacbio 105x | Chromosome | 1,878,827 | 1,878,922 | 38.5 | Yes | 99.99 |
8 6 |
96 | 0 |
| Wick et al. [14] | Klebsiella pneumoniae strain INF032 | Unicycler using Nanopore + Illumina 133x | Chromosome | 5,111,537 | 5,111,663 | 57.6 | Yes | 99.99 |
137 72 |
172 | 0 |
| Taylor et al. [54] |
Escherichia coli O157:H7 strain FSIS11705876 |
Unicycler using Nanopore + Illumina 692x |
Chromosome pO157 |
5,483,434 94,581 |
5,483,452 94,593 |
50.4 |
Yes Yes |
99.99 |
52 2 |
103 | 0 |
| Taylor et al. [54] | Salmonella enterica Bareilly strain CFSAN000189 | Unicycler using Nanopore + Illumina 599x |
Chromosome Plasmid |
4,724,806 81,814 |
4,724,797 81,815 |
52.2 |
Yes Yes |
99.99 |
32 21 |
34 | 0 |
|
SMRT Analysis v. 1.3.3 using PacBio RS 80x |
Chromosome Plasmid |
4,730,612 78,193 |
99.99 |
0 0 |
15 | 3 | |||||
| Bessonov et al. [55] | Salmonella enterica strain SA20055162 | Unicycler using Nanopore + Illumina 50x |
Chromosome Plasmid Plasmid |
4,640,729 |
4,640,715 105,679 98,127 |
51.7 |
Yes Yes Yes |
99.99 |
53 15 |
22 | 0 |
| Pitt et al [56] | Pandoraea fibrosis strain 6399 | Unicycler using Nanopore + Illumina 40x | Chromosome | 5,592,065 | 5,592,075 | 62.8 | Yes | 99.99 |
28 5 |
9 | 0 |
| Pitt et al. [56] | Pandoraea fibrosis strain 7641 | Unicycler using Nanopore + Illumina 20x | Chromosome | 5,592,064 | 5,591,941 | 62.8 | Yes | 99.99 |
81 15 |
102 | 0 |
| Sieber et al. [57] | Staphylococcus aureus strain 110900 | SPAdes using Nanopore + Illumina 334x |
Chromosome Plasmid unnamed |
2,918,239 2473 |
2,918,243 3356 |
32.7 |
Yes Yes |
99.99 |
6 6 |
5 | 0 |
| Sieber et al. [57] | Staphylococcus aureus strain 128254 | SPAdes using Nanopore + Illumina 219x |
Chromosome Plasmid unnamed |
2,877,083 2473 |
2,877,086 | 32.7 | Yes | 99.99 |
4 1 |
4 | 0 |
Flye was run using the --asm-coverage 100 parameter in order to reduce the computational run time. Only circular contigs are reported (as identified by Flye). For further details on all public data, see Supplementary dataset 1.