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Table 3 Hybrid assemblies of bacterial strains with real Illumina short reads and 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
Escherichia coli O26:H11 CFSAN027343 2 (2 cir.; 1 dead) 585 97 (3 cir.; 0 dead) 2 5,803,063 5,674,058 5,722,981 5,778,004 50.67 50.57 50.67 50.68
Escherichia coli O26:H11 CFSAN027350 5 (0 cir.; 2 dead) 488 108 (1 cir.; 0 dead) 2 5,604,298 5,512,883 5,522,347 5,593,613 50.65 50.53 50.57 50.64
Klebsiella variicola CFSAN086180 1 (1 cir.; 0 dead) 89 1 (1 cir.; 0 dead) 1 5,536,665 5,543,412 5,536,929 5,536,659 57.53 57.53 57.53 57.53
Klebsiella pneumonia CFSAN086181 1 (1 cir.; 0 dead) 56 1 (1 cir.; 0 dead) 1 5,221,910 5,230,821 5,221,909 5,221,909 57.58 57.53 57.58 57.58
Enterobacter cancerogenus CFSAN086183 2 (2 cir.; 0 dead) 113 2 (2 cir.; 0 dead) 2 4,990,691 5,003,034 4,992,376 4,992,376 55.59 55.56 55.59 55.59
Salmonella Bareilly CFSAN000189 2 (2 cir.; 0 dead) 80 2 (2 cir.; 0 dead) 2 4,806,601 4,816,325 4,806,603 4,808,805 52.21 52.23 52.21 52.22
Citrobacter braakii CFSAN086182 1 (1 cir.; 0 dead) 66 1 (1 cir.; 0 dead) 1 4,917,488 4,939,416 4,917,491 4,917,511 52.05 51.99 52.05 52.05
Cronobacter sakazakii CFSAN068773 3 (2 cir.; 1 dead) 75 4 (4 cir.; 0 dead) 4 4,577,802 4,597,231 4,581,781 4,581,781 56.73 56.71 56.73 56.73
Listeria monocytogenes CFSAN008100 2 (2 cir.; 1 dead) 18 2 (2 cir.; 0 dead) 2 3,102,056 3,140,938 3,137,527 3,108,102 37.95 37.91 37.90 37.91
Staphylococcus aureus CFSAN007894 4 (1 cir.; 6 dead) 75 3 (3 cir.; 0 dead) 2 2,749,203 2,774,416 2,763,803 2,757,659 32.86 32.92 32.82 32.84
Campylobacter jejuni CFSAN032806 2 (2 cir.; 0 dead) 55 2 (2 cir.; 0 dead) 2 1,811,805 1,774,178 1,814,450 1,782,911 30.53 30.67 30.54 30.53
Campylobacter coli CFSAN032805 3 (3 cir.; 0 dead) 51 3 (3 cir.; 0 dead) 3 1,750,134 1,765,016 1,750,172 1,750,177 31.41 31.56 31.41 31.41
  1. acir., circularized contigs
  2. bdead, dead ends