Table 4.
The performance comparison of our method on the loblolly pine dataset
| Correction method | Assembler | MA TPR | local MA TPR | FPR |
|---|---|---|---|---|
| misSEQuel | ABySS | 31% (40/127) | 57% (405/715) | 43% (1604/3754) |
| SPAdes (−rr) | 100% (7/7) | 73% (8/11) | <1% (135/20 653) | |
| SPAdes (+rr) | 67% (199/299) | 67% (38/57) | 38% (3117/8254) | |
| IDBA | 52% (32/61) | 73% (145/200) | 19% (4258/22 150) | |
| REAPR | ABySS | 7% (9/127) | 2% (12/715) | 3% (112/3754) |
| SPAdes (−rr) | 14% (1/7) | 27% (3/11) | 6% (1323/20 653) | |
| SPAdes (+rr) | 7% (21/299) | 5% (3/57) | 5% (424/8254) | |
| IDBA | 2% (1/61) | 6% (12/200) | 11% (2354/22 150) | |
| Pilon | ABySS | 7% (8/127) | 2% (11/715) | 2% (70/3754) |
| SPAdes (−rr) | 14% (1/7) | 18% (2/11) | 4% (923/20 653) | |
| SPAdes (+rr) | 5% (16/299) | 5% (3/57) | 5% (388/8254) | |
| IDBA | 2% (1/61) | 5% (12/200) | 8% (1823/22 150) |
Again, a true positive in this context is a contig that is misassembled and is predicted to be so. A false positive is a correctly assembled contig that was predicted to be misassembled. Bold values highlight MISSEQUEL results.