Table 2.
Benchmarking of hybridSPAdes and selfPBcR on down-sampled ECOLI200 datasets with reduced coverage by long reads
|
ECOLI200 |
|||||
|---|---|---|---|---|---|
| LG50 | NG50 | NG75 | longest | MA | |
| hybridSPAdes 200× | 1 | 4652737 | 4652737 | 4652737 | 7 |
| selfPBcR 200× | 1 | 4680888 | 4680888 | 4680888 | 8 |
| hybridSPAdes 100× | 1 | 4652556 | 4652556 | 4652556 | 7 |
| selfPBcR 100× | 1 | 4677843 | 4677843 | 4677843 | 8 |
| hybridSPAdes 50× | 1 | 4652375 | 4652375 | 4652375 | 7 |
| selfPBcR 50× | 3 | 758477 | 494886 | 876582 | 9 |
| hybridSPAdes 25× | 1 | 2643623 | 1817256 | 2643623 | 7 |
| selfPBcR 25× | – | – | – | 82951 | 6 |
| hybridSPAdes 12.5× | |||||
| (Illumina + PacBio) | 1 | 3398297 | 746845 | 3398297 | 9 |
| selfPBcR 12.5× | – | – | – | 15884 | 0 |
| hybridSPAdes 6.25× | 5 | 356505 | 210465 | 692018 | 9 |
| selfPBcR 6.25× | – | – | – | – | – |
The coverage was downsampled from 200× to 6.25×. NG50, LG50 and NG75 are not defined for PBcR assembly with coverage 25× and lower because the total assembly length is less than half of the genome length. For coverage 6.25×, PBcR failed to generate an assembly.