Table 2.
Recovery rates of small (< 10 kb), medium (10 kb – 99 kb), and large (≥ 100 kb) bacterial plasmids by long- and short-reads-first genome assemblers in replicate genome assemblies (n=3). The total percent plasmid recovery is shown, along with the percentage of recovered plasmids that were erroneously identified in the chromosome or present as multiple copies in a single assembly
|
% Plasmids Recovered |
||||
|
Plasmid Size |
Assembler |
Total |
In Chromsome |
Multiplicated |
|
Large (≥ 100 kb) (n=18) |
Flye-hq |
100 |
0 |
0 |
|
Flye-meta |
100 |
0 |
0 |
|
|
Flye-raw |
100 |
0 |
0 |
|
|
Miniasm |
89 |
6 |
0 |
|
|
Raven |
100 |
0 |
0 |
|
|
Canu |
83 |
0 |
0 |
|
|
Unicycler |
100 |
0 |
0 |
|
|
Medium (99 kb – 10 kb) (n=48) |
Flye-hq |
100 |
0 |
0 |
|
Flye-meta |
100 |
0 |
0 |
|
|
Flye-raw |
96 |
0 |
4 |
|
|
Miniasm |
100 |
2 |
4 |
|
|
Raven |
92 |
0 |
0 |
|
|
Canu |
98 |
0 |
13 |
|
|
Unicycler |
100 |
0 |
0 |
|
|
Small (> 10 kb) (n=33) |
Flye-hq |
67 |
0 |
0 |
|
Flye-meta |
73 |
0 |
0 |
|
|
Flye-raw |
79 |
0 |
0 |
|
|
Miniasm |
64 |
0 |
29 |
|
|
Raven |
39 |
0 |
0 |
|
|
Canu |
100 |
0 |
36 |
|
|
Unicycler |
100 |
0 |
0 |
|