Table 2.
Hybrid assemblies of bacterial strains with simulated Illumina short reads and low-quality Oxford Nanopore long reads using MaSuRCA, SPAdes, and Unicycler
| Strain | Number of contigs | Total length (bp) | GC content (%) | ||||||
|---|---|---|---|---|---|---|---|---|---|
| MaSuRCA | SPAdes | Unicycler | MaSuRCA | SPAdes | Unicycler | MaSuRCA | SPAdes | Unicycler | |
| Pseudomonas aeruginosa PAO1 | 4 (0 cir.; 8 dead) | 64 | 1 (0 cir.; 2 dead) | 6,173,430 | 6,261,368 | 6,264,384 | 66.55 | 66.57 | 66.56 |
| Escherichia coli O157:H7 Sakai | 6 (0 cir.; 12 dead) | 550 | 83 (0 cir.; 6 dead) | 5,503,884 | 5,487,649 | 5,562,446 | 50.50 | 50.38 | 50.45 |
| Bacillus anthracis Ames Ancestor | 7 (0 cir.; 14 dead) | 78 | 3 (0 cir.; 6 dead) | 5,433,227 | 5,482,457 | 5,489,222 | 35.26 | 35.17 | 35.23 |
| Klebsiella variicola DSM 15968 | 1 (0 cir.; 2 dead) | 121 | 1 (0 cir.; 2 dead) | 5,482,918 | 5,505,259 | 5,520,752 | 57.54 | 57.57 | 57.56 |
| Salmonella Typhimurium LT2 | 3 (0 cir.; 6 dead) | 78 | 3 (0 cir.; 3 dead) | 4,848,561 | 4,952,963 | 4,947,288 | 52.22 | 52.24 | 52.24 |
| Cronobacter sakazakii ATCC 29544 | 18 (0 cir.; 36 dead) | 72 | 4 (1 cir.; 6 dead) | 4,492,402 | 4,640,822 | 4,663,144 | 56.60 | 56.67 | 56.64 |
| Clostridium botulinum CDC_1632 | 2 (1 cir.; 2 dead) | 109 | 11 (0 cir.; 2 dead) | 4,398,971 | 4,379,115 | 4,372,396 | 28.04 | 27.95 | 27.92 |
| Listeria monocytogenes EGD-e | 4 (1 cir.; 6 dead) | 11 | 1 (0 cir.; 2 dead) | 2,927,219 | 2,933,282 | 2,942,862 | 38.02 | 37.94 | 37.97 |
| Staphylococcus aureus NCTC 8325 | 3 (0 cir.; 6 dead) | 37 | 1 (0 cir.; 2 dead) | 2,759,087 | 2,818,488 | 2,821,119 | 32.88 | 32.84 | 32.87 |
| Campylobacter jejuni NCTC 11168 | 1 (0 cir.; 2 dead) | 8 | 1 (0 cir.; 2 dead) | 1,630,638 | 1,640,924 | 1,641,330 | 30.56 | 30.55 | 30.55 |
acir., circularized contigs
bdead, dead ends