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

Table 1 Hybrid assemblies of bacterial strains with simulated Illumina short reads and mediocre-quality Oxford Nanopore long reads using MaSuRCA, SPAdes, and Unicycler compared to their corresponding reference genomes

Strain	Number of contigs				Total length (bp)				GC content (%)
Strain	MaSuRCA	SPAdes	Unicycler	Reference	MaSuRCA	SPAdes	Unicycler	Reference	MaSuRCA	SPAdes	Unicycler	Reference
Pseudomonas aeruginosa PAO1	1 (0 cir.; 2 dead)	39	1 (0 cir.; 2 dead)	1	6,264,321	6,261,361	6,264,377	6,264,404	66.56	66.57	66.56	66.56
Escherichia coli O157:H7 Sakai	2 (0 cir.; 4 dead)	456	3 (0 cir.; 6 dead)	3	5,591,228	5,518,282	5,594,148	5,594,605	50.49	50.40	50.48	50.48
Bacillus anthracis Ames Ancestor	3 (0 cir.; 6 dead)	47	3 (0 cir.; 6 dead)	3	5,503,594	5,508,786	5,489,222	5,503,926	35.24	35.25	35.23	35.24
Klebsiella variicola DSM 15968	1 (0 cir.; 2 dead)	38	1 (0 cir.; 2 dead)	1	5,521,107	5,517,301	5,521,041	5,521,203	57.56	57.57	57.56	57.56
Salmonella Typhimurium LT2	2 (0 cir.; 4 dead)	43	3 (0 cir.; 3 dead)	2	4,951,226	4,956,436	4,947,278	4,951,383	52.24	52.24	52.24	52.24
Cronobacter sakazakii ATCC 29544	3 (1 cir.; 4 dead)	54	4 (1 cir.; 6 dead)	4	4,658,297	4,642,775	4,663,118	4,663,565	56.64	56.67	56.64	56.64
Clostridium botulinum CDC_1632	2 (1 cir.; 2 dead)	86	1 (0 cir.; 2 dead)	1	4,398,971	4,393,287	4,392,893	4,393,047	28.04	28.01	28.02	28.02
Listeria monocytogenes EGD-e	2 (1 cir.; 2 dead)	7	1 (0 cir.; 2 dead)	1	2,950,445	2,944,768	2,944,366	2,944,528	38.01	37.98	37.98	37.98
Staphylococcus aureus NCTC 8325	1 (0 cir.; 2 dead)	47	1 (0 cir.; 2 dead)	1	2,821,292	2,825,487	2,821,211	2,821,361	32.87	32.87	32.87	32.87
Campylobacter jejuni NCTC 11168	1 (0 cir.; 2 dead)	2	1 (0 cir.; 2 dead)	1	1,641,372	1,641,539	1,641,262	1,641,481	30.55	30.55	30.55	30.55

ISSN: 1471-2164