Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

Table 7 Numbers of virulence genes of bacterial strains with simulated Illumina short reads and low-quality Oxford Nanopore long reads, as predicted based on their MaSuRCA, SPAdes, and Unicycler assemblies

Strain	Number of virulence genes
Strain	MaSuRCA	SPAdes	Unicycler
Pseudomonas aeruginosa PAO1	184	184	184
Escherichia coli O157:H7 Sakai	110	128	128
Bacillus anthracis Ames Ancestor	13	13	13
Klebsiella variicola DSM 15968	10	10	10
Salmonella Typhimurium LT2	107	117	118
Cronobacter sakazakii ATCC 29544	2	2	2
Clostridium botulinum CDC_1632	0	0	0
Listeria monocytogenes EGD-e	32	32	32
Staphylococcus aureus NCTC 8325	62	63	63
Campylobacter jejuni NCTC 11168	118	119	118

ISSN: 1471-2164