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

Table 8 Numbers of virulence genes of bacterial strains with real Illumina short reads and Oxford Nanopore long reads, as predicted based on their MaSuRCA, SPAdes, and Unicycler assemblies and compared to their corresponding reference genomes

Strain	Numbers of virulence genes
Strain	MaSuRCA	SPAdes	Unicycler	Reference
Escherichia coli O26:H11 CFSAN027343	115	115	114	121
Escherichia coli O26:H11 CFSAN027350	110	108	109	115
Klebsiella variicola CFSAN086180	10	10	10	10
Klebsiella pneumonia CFSAN086181	10	10	10	10
Enterobacter cancerogenus CFSAN086183	15	15	15	16
Salmonella Bareilly CFSAN000189	109	109	109	111
Citrobacter braakii CFSAN086182	23	23	23	22
Cronobacter sakazakii CFSAN068773	2	2	2	4
Listeria monocytogenes CFSAN008100	31	31	31	32
Staphylococcus aureus CFSAN007894	63	63	63	63
Campylobacter jejuni CFSAN032806	104	105	104	107
Campylobacter coli CFSAN032805	76	76	76	77

ISSN: 1471-2164