TABLE 3.
Comparison of Quast metrics number of contigs and N50 value between the hybrid assembly (internal reference) and the four assemblers used.
| Isolate information |
Hybrid assembly |
Canu |
Flye |
Miniasm |
Raven |
||||||
| Isolate ID | Species | No contigs | N50 | No contigs | N50 | No contigs | N50 | No contigs | N50 | No contigs | N50 |
| MIN-005 | Acinetobacter baumannii | 12 | 3,525,656 | 75 | 2,633,785 | 8 | 3,964,326 | 60 | 2,774,148 | 12 | 3,998,627 |
| MIN-010 | Acinetobacter baumannii | 7 | 3,820,548 | 116 | 1,911,802 | 4 | 3,819,441 | 4 | 3,817,982 | 4 | 3,818,776 |
| MIN-012 | Acinetobacter baumannii | 4 | 3,878,733 | 25 | 797,795 | 5 | 3,873,279 | 23 | 346,264 | 14 | 882,722 |
| MIN-021 | Burkholderia cenocepacia | 5 | 2,953,509 | 33 | 3,020,397 | 4 | 2,996,827 | 4 | 3,006,784 | 5 | 2,996,894 |
| MIN-029 | Enterobacter asburiae | 11 | 3,233,646 | 23 | 4,799,594 | 5 | 4,785,704 | 12 | 4,785,894 | 6 | 4,682,746 |
| MIN-030 | Enterobacter hormaechei | 4 | 4,716,358 | 37 | 4,576,092 | 3 | 4,714,883 | 8 | 4,263,122 | 3 | 4,715,059 |
| MIN-036 | Escherichia coli | 6 | 4,928,993 | 166 | 3,944,955 | 7 | 4,927,117 | 3 | 4,927,923 | 3 | 4,926,621 |
| MIN-040 | Escherichia coli | 4 | 4,514,829 | 6 | 4,677,337 | 2 | 4,652,244 | 2 | 4,652,852 | 2 | 4,652,280 |
| MIN-049 | Escherichia coli | 5 | 4,768,909 | 40 | 4,791,838 | 5 | 4,769,105 | 3 | 4,773,444 | 5 | 4,769,200 |
| MIN-073 | Escherichia coli | 12 | 4,742,845 | 12 | 4,754,605 | 6 | 4,744,646 | 7 | 4,743,179 | 4 | 4,698,004 |
| MIN-088 | Raoultella ornithinolytica | 4 | 5,399,857 | 79 | 5,416,040 | 6 | 5,398,098 | 18 | 4,815,076 | 5 | 5,106,679 |
| MIN-106 | Klebsiella pneumoniae | 8 | 5,300,304 | 140 | 5,323,728 | 6 | 5,297,916 | 235 | 5,298,979 | 6 | 5,298,450 |
| MIN-119 | Klebsiella pneumoniae | 11 | 5,054,824 | 113 | 5,124,097 | 5 | 5,103,142 | 113 | 5,103,754 | 5 | 5,103,899 |
| MIN-129 | Klebsiella quasipneumoniae | 20 | 5,038,265 | 91 | 5,283,547 | 6 | 5,255,931 | 5 | 5,258,770 | 3 | 5,258,391 |
| MIN-132 | Mycoplasma hominis | 1 | 708,710 | 13 | 50,339 | 1 | 707,499 | 9 | 40,375 | 11 | 73,132 |
| MIN-137 | Pseudomonas aeruginosa | 2 | 6,531,433 | 9 | 4,840,050 | 2 | 6,527,025 | 5 | 2,736,100 | 2 | 5,810,542 |
| MIN-156 | Pseudomonas putida | 3 | 5,944,170 | 6 | 6,185,656 | 2 | 6,167,022 | 1 | 6,167,466 | 1 | 6,167,000 |
| MIN-160 | Salmonella enterica | 2 | 4,634,052 | 20 | 4,748,104 | 2 | 4,726,543 | 2 | 4,727,634 | 3 | 4,726,892 |
| MIN-164 | Serratia marcescens | 2 | 5,099,060 | 18 | 1,973,127 | 2 | 5,096,271 | 2 | 5,097,058 | 2 | 5,096,789 |
| MIN-169 | Staphylococcus aureus | 2 | 2,792,307 | 73 | 25,754 | 41 | 86,444 | 5 | 27,339 | 39 | 32,652 |
| MIN-176 | Staphylococcus sciuri | 1 | 2,933,004 | 11 | 2,954,979 | 1 | 2,932,657 | 1 | 2,933,161 | 1 | 2,933,014 |
| MIN-182 | Streptococcus agalactiae | 2 | 2,024,578 | 14 | 711,413 | 1 | 2,140,986 | 3 | 2,059,889 | 2 | 2,062,716 |
| MIN-189 | Streptococcus agalactiae | 3 | 2,185,475 | 9 | 2,263,670 | 1 | 2,239,484 | 1 | 2,238,695 | 2 | 2,180,722 |
| MIN-198 | Ureaplasma parvum | 1 | 726,862 | 20 | 717,827 | 1 | 726,458 | 6 | 726,694 | 3 | 726,167 |
| MIN-201 | Ureaplasma urealyticum | 1 | 816,741 | 4 | 834,700 | 1 | 816,472 | 1 | 816,845 | 1 | 816,642 |
Data represent an average of the metrics produced from the Filtlong and Nanofilt assemblies.