Table 3 De novo assembly of clinical E. coli strains with ONT reads using Flye, Canu, Wtdbg2, and NECAT assemblers with and without read correcting with Medaka, NextPolish, and Racon. M = Medaka, NP = NextPolish, R = Racon. Bold = highest number, underline = lowest number, NA = not applicable
Assembler | Flye | Canu | Wtdbg2 | NECAT | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Read correction | - | M | NP | R | - | M | NP | R | - | M | NP | R | - | M | NP | R | ||
Total length (bp) | ||||||||||||||||||
 Barcode01 | 5,469,936 | 5,478,602 | 5,539,345 | 5,475,629 | 5,579,075 | 5,593,923 | 5,579,075 | 5,589,830 | 4,715,179 | 4,732,533 | 4,715,179 | 4,729,394 | 5,459,846 | 5,467,399 | 5,459,846 | 5,463,665 | ||
 Barcode02 | 5,066,917 | 5,080,864 | 5,066,917 | 5,075,921 | 4,615,621 | 4,638,920 | 4,615,621 | 4,632,707 | 3,359,552 | 3,477,009 | 3,359,552 | 3,465,773 | NA | NA | NA | NA | ||
 Barcode03 | 5,294,465 | 5,302,241 | 5,294,465 | 5,300,744 | 5,303,012 | 5,315,872 | 5,303,012 | 5,314,629 | 5,213,454 | 5,238,851 | 5,213,454 | 5,237,108 | 5,314,925 | 5,320,631 | 5,314,925 | 5,318,958 | ||
 Barcode04 | 5,247,697 | 5,256,000 | 5,247,697 | 5,253,316 | 5,369,978 | 5,385,202 | 5,369,978 | 5,381,812 | 4,220,087 | 4,244,567 | 4,220,087 | 4,236,146 | 5,208,954 | 5,215,762 | 5,208,954 | 5,212,343 | ||
 Barcode06 | 5,476,326 | 5,484,941 | 5,476,326 | 5,483,418 | 5,530,456 | 5,545,123 | 5,530,456 | 5,542,970 | 5,410,478 | 5,437,044 | 5,410,478 | 5,434,446 | 5,475,891 | 5,482,890 | 5,475,891 | 5,481,005 | ||
 Barcode08 | 9,671,007 | 9,682,127 | 9,671,007 | 9,654,206 | 5,988,291 | 6,026,955 | 5,988,291 | 6,010,588 | 4,369,074 | 4,529,659 | 4,369,074 | 4,508,127 | NA | NA | NA | NA | ||
 Barcode09 | 7,253,462 | 7,269,121 | 7,253,462 | 7,244,915 | 7,482,615 | 7,521,371 | 7,482,615 | 7,504,387 | 6,279,759 | 6,386,039 | 6,279,759 | 6,354,810 | 6,253,465 | 6,278,638 | 6,253,465 | 6,254,786 | ||
 Barcode11 | 4,892,227 | 4,899,205 | 4,892,227 | 4,899,245 | 4,977,509 | 4,988,711 | 4,977,509 | 4,988,061 | 5,046,387 | 5,073,001 | 5,046,387 | 5,050,697 | 4,648,910 | 4,653,507 | 4,648,910 | 4,653,170 | ||
 Barcode12 | 5,515,594 | 5,520,560 | 5,511,890 | 5,517,067 | 5,709,957 | 5,725,656 | 5,709,957 | 5,721,016 | 5,329,936 | 5,365,151 | 5,329,936 | 5,359,875 | 5,409,945 | 5,417,213 | 5,409,945 | 5,412,674 | ||
Number of contigs | ||||||||||||||||||
 Barcode01 | 5 | 5 | 5 | 5 | 7 | 7 | 7 | 7 | 7 | 7 | 7 | 7 | 3 | 3 | 3 | 3 | ||
 Barcode02 | 126 | 128 | 126 | 128 | 207 | 207 | 207 | 207 | 127 | 127 | 127 | 127 | NA | NA | NA | NA | ||
 Barcode03 | 6 | 6 | 6 | 6 | 3 | 3 | 3 | 3 | 9 | 9 | 9 | 9 | 8 | 8 | 8 | 8 | ||
 Barcode04 | 13 | 13 | 13 | 13 | 12 | 12 | 12 | 12 | 14 | 14 | 14 | 13 | 13 | 13 | 13 | 13 | ||
 Barcode06 | 11 | 11 | 11 | 11 | 6 | 6 | 6 | 6 | 17 | 17 | 17 | 17 | 6 | 6 | 6 | 6 | ||
 Barcode08 | 357 | 358 | 357 | 356 | 537 | 539 | 537 | 537 | 209 | 209 | 209 | 209 | NA | NA | NA | NA | ||
 Barcode09 | 137 | 137 | 137 | 137 | 127 | 127 | 127 | 127 | 79 | 79 | 79 | 78 | 108 | 108 | 108 | 108 | ||
 Barcode11 | 1 | 1 | 1 | 1 | 10 | 10 | 10 | 10 | 12 | 12 | 12 | 9 | 1 | 1 | 1 | 1 | ||
 Barcode12 | 18 | 16 | 16 | 16 | 15 | 15 | 15 | 15 | 11 | 11 | 11 | 11 | 20 | 20 | 20 | 20 | ||
GC% | ||||||||||||||||||
 Barcode01 | 50.74 | 50.74 | 50.78 | 50.73 | 50.72 | 50.72 | 50.72 | 50.71 | 50.74 | 50.73 | 50.74 | 50.71 | 50.75 | 50.76 | 50.75 | 50.75 | ||
 Barcode02 | 50.92 | 50.92 | 50.92 | 50.89 | 50.84 | 50.93 | 50.84 | 50.88 | 51.5 | 51.22 | 51.5 | 51.1 | NA | NA | NA | NA | ||
 Barcode03 | 50.8 | 50.79 | 50.8 | 50.79 | 50.82 | 50.81 | 50.82 | 50.81 | 50.81 | 50.78 | 50.81 | 50.77 | 50.8 | 50.8 | 50.8 | 50.8 | ||
 Barcode04 | 50.66 | 50.65 | 50.66 | 50.64 | 50.75 | 50.75 | 50.75 | 50.74 | 50.49 | 50.46 | 50.49 | 50.43 | 50.64 | 50.65 | 50.64 | 50.63 | ||
 Barcode06 | 50.57 | 50.56 | 50.57 | 50.56 | 50.48 | 50.47 | 50.48 | 50.46 | 50.52 | 50.51 | 50.52 | 50.49 | 50.5 | 50.5 | 50.5 | 50.49 | ||
 Barcode08 | 52.9 | 52.88 | 52.9 | 52.79 | 53.15 | 53.15 | 53.15 | 53.03 | 54.61 | 53.96 | 54.61 | 53.46 | NA | NA | NA | NA | ||
 Barcode09 | 50.21 | 50.13 | 50.21 | 50.06 | 50.68 | 50.68 | 50.68 | 50.62 | 50.49 | 50.41 | 50.49 | 50.28 | 50.71 | 50.7 | 50.71 | 50.66 | ||
 Barcode11 | 50.85 | 50.84 | 50.85 | 50.84 | 50.77 | 50.76 | 50.77 | 50.76 | 50.75 | 50.72 | 50.75 | 50.7 | 50.95 | 50.95 | 50.95 | 50.94 | ||
 Barcode12 | 22 | 50.39 | 50.4 | 50.38 | 22 | 50.38 | 50.39 | 50.37 | 11 | 50.44 | 50.47 | 50.41 | 18 | 50.36 | 50.35 | 50.34 | ||
Total aligned (bp) | ||||||||||||||||||
 Barcode01 | 4,153,701 | 4,131,518 | 2,489,913 | 4,088,076 | 4,089,970 | 4,149,790 | 4,089,969 | 4,098,541 | 3,435,260 | 3,582,022 | 3,435,144 | 3,513,526 | 4,072,587 | 4,137,015 | 4,072,586 | 4,073,699 | ||
 Barcode02 | 4,234,234 | 4,223,032 | 4,234,231 | 4,149,381 | 3,614,373 | 3,805,118 | 3,614,371 | 3,730,664 | 1,115,774 | 2,732,632 | 1,115,774 | 2,757,655 | NA | NA | NA | NA | ||
 Barcode03 | 4,450,464 | 4,430,100 | 4,450,464 | 4,410,942 | 4,405,608 | 4,441,610 | 4,405,608 | 4,426,312 | 4,140,253 | 4,385,142 | 4,140,253 | 4,370,266 | 4,385,814 | 4,443,930 | 4,385,814 | 4,415,394 | ||
 Barcode04 | 4,223,485 | 4,182,278 | 4,223,485 | 4,163,481 | 4,152,322 | 4,204,149 | 4,152,322 | 4,165,641 | 3,217,785 | 3,470,346 | 3,217,785 | 3,432,050 | 4,096,702 | 4,189,276 | 4,096,702 | 4,153,810 | ||
 Barcode06 | 4,430,645 | 4,406,775 | 4,430,645 | 4,376,047 | 4,365,538 | 4,409,083 | 4,365,339 | 4,372,342 | 4,147,601 | 4,375,901 | 4,147,601 | 4,336,730 | 4,289,285 | 4,396,616 | 4,289,128 | 4,355,667 | ||
 Barcode08 | 3,949,545 | 3,951,123 | 3,949,544 | 3,955,591 | 2,610,245 | 2,669,926 | 2,610,245 | 2,667,499 | 335,832 | 1,185,183 | 335,832 | 1,391,558 | NA | NA | NA | NA | ||
 Barcode09 | 4,679,828 | 4,626,706 | 4,679,828 | 4,590,052 | 5,601,691 | 5,633,641 | 5,601,691 | 5,502,302 | 3,426,173 | 4,258,633 | 3,426,173 | 4,304,669 | 4,593,133 | 4,669,739 | 4,593,133 | 4,621,159 | ||
 Barcode11 | 4,126,820 | 4,107,981 | 4,126,846 | 4,082,815 | 4,074,616 | 4,104,945 | 4,074,642 | 4,069,038 | 3,915,825 | 4,109,486 | 3,915,851 | 4,067,450 | 3,873,085 | 3,909,040 | 3,873,111 | 3,873,759 | ||
 Barcode12 | 4,110,855 | 4,086,413 | 4,110,855 | 4,065,379 | 4,057,280 | 4,105,650 | 4,057,280 | 4,081,821 | 3,656,460 | 4,072,434 | 3,656,453 | 4,025,549 | 3,966,073 | 4,045,206 | 3,965,670 | 4,009,086 | ||
Indels | ||||||||||||||||||
 Barcode01 | 3369 | 4497 | 9003 | 5765 | 6088 | 4475 | 6088 | 6026 | 8020 | 4006 | 8019 | 5368 | 6899 | 4601 | 6899 | 5946 | ||
 Barcode02 | 3363 | 4484 | 3363 | 6801 | 11,882 | 4379 | 11,882 | 7155 | 12,724 | 7131 | 12,724 | 6097 | NA | NA | NA | NA | ||
 Barcode03 | 3094 | 4423 | 3094 | 5826 | 6265 | 4379 | 6265 | 6080 | 13,714 | 4438 | 13,714 | 6120 | 8115 | 4581 | 8115 | 6020 | ||
 Barcode04 | 3031 | 4129 | 3031 | 5484 | 6350 | 4004 | 6350 | 5771 | 11,303 | 3634 | 11,303 | 5024 | 8076 | 4348 | 8076 | 5687 | ||
 Barcode06 | 3197 | 4403 | 3197 | 6135 | 6346 | 4327 | 6346 | 6290 | 12,523 | 4587 | 12,523 | 6527 | 8256 | 4613 | 8254 | 6251 | ||
 Barcode08 | 7221 | 7447 | 7221 | 9096 | 8513 | 4225 | 8513 | 6916 | 4077 | 4412 | 4077 | 4924 | NA | NA | NA | NA | ||
 Barcode09 | 7054 | 8617 | 7054 | 10,217 | 13,117 | 10,696 | 13,117 | 14,279 | 24,432 | 11,822 | 24,431 | 10,949 | 11,868 | 8790 | 11,868 | 11,192 | ||
 Barcode11 | 2867 | 3990 | 2867 | 5678 | 5206 | 3837 | 5206 | 5731 | 9919 | 4053 | 9919 | 5821 | 6519 | 3942 | 6519 | 5394 | ||
 Barcode12 | 3232 | 4313 | 3253 | 5451 | 3648.64 | 4338 | 6042 | 5714 | 3537.49 | 4819 | 15,282 | 5811 | 3616.25 | 4626 | 7715 | 5691 | ||