| | MECAT Raw | MiniScrub + MECAT | Canu Raw | MiniScrub + Canu |
|---|
% genome assembled | 79.39% |
99.86%
| 99.69% |
99.71%
|
NGA50 | 242478 |
1053459
|
1055037
| 696460 |
LGA50 | 12 |
3
|
2
| 5 |
# of contigs | 38 |
11
|
7
| 19 |
# mis-assembled contigs | 28 |
5
| 2 | 2 |
# local mis-assemblies | 209 |
4
| 5 |
3
|
# indels > 5 bp | 1099 |
394
| 84 |
46
|
Runtime (hours) |
2.5
| 9 | 80 |
9
|
- MiniScrub significantly improves assembly, tested with MECAT [32], increasing genome coverage and NGA50 while limiting LGA50, mis-assemblies, mismatches, and indels. Canu’s assembly had slightly reduced errors and misassemblies when reads were preprocessed with MiniScrub, but the assembly was more fractured, likely due in part to resolving large misassemblies and indels. Notably, Canu assembly of raw reads took about 3.5 days, while the MiniScrub+Canu pipeline took about 9 hours, likely due to a reduction in the amount of error correction needed in the latter situation. Results were evaluated using QUAST [33] Best performance numbers are shown in bold
