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
| 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 |
acir., circularized contigs
bdead, dead ends