Table 1 Top blast hit, coverage and identity of contigs assembled by the Miniasm and Flye assemblers. For the Flye assembler, several settings, default, meta and plasmid, were tested. The samples represent 12 plasmid DNA extracts that contained multiple multidrug resistance-encoding plasmids and were published previously. *, newly assembled with the Flye assembler using the meta option; **, average coverage and identity of plasmids that could be assembled and had a BLAST hit
Sample | Top BLAST hit | Size (bp) | Assembler Size (bp) coverage (%)/identity (%) | |||
|---|---|---|---|---|---|---|
Miniasm | Flye | metaFlye | plasmidFlye | |||
RB01 | RB01-LZ135-CTX-128976 | 128,976 | 127,607 99/98.5 | 128,991 100/99.2 | 128,925 100/99.2 | 128,962 100/99.2 |
RB01 | RB01-LZ135-NDM-90845 | 90,845 | 172,204 100/98.0 | 91,325 99/98.9 | 91,353 99/98.9 | 91,353 100/98.9 |
RB02 | RB02-JN105-IncN-CTX-139496-N | 142,307 | 143,553 99/96.3 | 117,855 100/96.7 | 144,482 99/96.6 | 117,851 81/96.7 |
RB02 | RB02-JN105-IncF-TET-116277-N | 116,277 | 119,228 99/97.9 | 119,956 99/97.8 | 119,986 99/97.8 | 119.936 99/96.7 |
RB02 | RB02-JN105-IncY-CTX-98443 | 98,443 | 98,276 99/98.7 | 98,754 100/98.9 | 99,197 100/98.8 | 99,043 100/98.3 |
RB02 | RB02-JN105-IncN-NDM6–55342 | 55,342 | 64,116 99/84.2 | 56,170 98/83.7 | 62,679 99/83.6 | 56,172 98/83.9 |
RB02 | RB02-JN105-IncX-NDM5–45823 | 45,823 | 46,253 100/97.7 | 37,738 100/98.0 | 46,466 99/98.6 | 37,767 99/98.6 |
RB03 | RB03-WH96T-IncF-OXA-153088 | 153,088 | 152,062 99/98.5 | 150,101 99/98.1 | 150,051 100/99.1 | 150,093 99/99.1 |
RB03 | RB03-WH96T-IncN-NDM1–56215 | 56,215 | 58,008 100/98.5 | 52,703 98/98.9 | 56,496 100/98.9 | 52,711 98/98.9 |
RB04 | RB04-SZ584-1 T-IncY-130,821 | 130,821 | 133,587 99/97.4 | 134,643 99/96.9 | 134,537 99/96.7 | – |
RB04 | RB04-SZ584-1 T-IncF-TET-114056 | 114,065 | 111,330 99/98.5 | 114,409 100/99.2 | 114,405 100/99.0 | 114,434 100/98.9 |
RB04 | RB04-SZ584-1 T-IncX3-NDM1-56 K-NC | 55,919 | 214,172 99/95.4 | 10,965 10/NA | 234,535 100/95.7 | 5,036 10/NA |
RB04 | RB04-234 K-Flye* | 234,535 | 214,172 90/98.0 | – | 234,535 100/100 | – |
RB05 | RB05-C267-IncA/C-CTX-166467 | 166,467 | 165,709 97/98.9 | 313,534 100/98.9 | 166,440 100/99.3 | 313,534 100/98.9 |
RB06 | RB06-C499-IncA/C-CTX-192739 | 192,739 | 191,256 99/98.7 | 192,983 100/98.9 | 192,728 100/99.3 | 192,720 100/98.9 |
RB07 | RB07-vb0506-IncA/C-CTX-133742 | 133,742 | 130,025 94/98.6 | – | 133,339 100/97.6 | – |
RB09 | RB09-IncN-KPC-68571 | 68,571 | 133,828 99/98.6 | 68,899 99/98.9 | 68,904 99/98.9 | 68,895 99/98.9 |
RB10 | RB10-29KPC-IncF-TET-136532 | 136,532 | 133,611 98/98.8 | 136,726 100/99.3 | 136,713 100/99.3 | 136,710 100/99.3 |
RB10 | RB10-29KPC-IncY-KPC-98 K-N | 95,908 | 96,533 95/98.5 | 97,091 99/98.1 | 97,602 99/98.1 | 97,528 99/98.2 |
RB11 | RB11-IncF-IncHI-KPC-238153 | 238,153 | 238,205 99/98.4 | 255,475 100/98.8 | 229,070 100/98.8 | 239,791 100/98.8 |
RB12 | RB12-74 T-KPC-IncF-115 K-N | 115,689 | 117,851 98/98.0 | 118,528 99/97.8 | 111,151 94/97.8 | 118,574 99/97.8 |
RB12 | RB12-74 T-KPC-IncN-IncX1-KPC-108 K-N | 107,969 | 108,968 96/97.7 | 104,277 100/97.3 | 110,786 100/97.5 | 104,278 94/97.4 |
Average coverage/identity** | 98.2/97.5 | 95.1/97.6 | 99.4/97.7 | 93.5/97.7 | ||