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 |