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Table 2 MicroPIPE v0.9 results for public datasets

From: MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction

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
  1. 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.