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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

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

Strain Number of contigs Total length (bp) GC content (%)
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
  1. acir., circularized contigs
  2. bdead, dead ends