Table 2.
The performance comparison of our method on the F.tularensis dataset
| Correction method | Assembler | MA TPR | local MA TPR | FPR |
|---|---|---|---|---|
| misSEQuel (paired-end data only) | Velvet | 100% (11/11) | 100% (36/36) | 58% (180/312) |
| SOAPdenovo | 100% (10/10) | 100% (35/35) | 63% (165/263) | |
| ABySS | 100% (64/64) | 100% (32/32) | 87% (20/23) | |
| SPAdes (−rr) | 100% (11/11) | 100% (30/30) | 83% (52/63) | |
| SPAdes (++rr) | 100% (23/23) | 100% (31/31) | 86% (49/57) | |
| IDBA | 100% (10/10) | 100% (31/31) | 38% (57/149) | |
| misSEQuel (optical mapping data only) | Velvet | 55% (6/11) | 69% (25/36) | 24% (76/312) |
| SOAPdenovo | 80% (8/10) | 63% (22/35) | 29% (77/263) | |
| ABySS | 69% (44/64) | 88% (28/32) | 13% (3/23) | |
| SPAdes (−rr) | 91% (10/11) | 87% (26/30) | 21% (13/63) | |
| SPAdes (++rr) | 87% (20/23) | 81% (25/31) | 16% (9/57) | |
| IDBA | 90% (9/10) | 77% (24/31) | 10% (15/149) | |
| misSEQuel (paired-end and optical mapping data) | Velvet | 55% (6/11) | 100% (36/36) | 22% (68/312) |
| SOAPdenovo | 80% (8/10) | 84% (21/35) | 20% (53/263) | |
| ABySS | 69% (44/64) | 88% (28/32) | 13% (3/23) | |
| SPAdes (−rr) | 91% (10/11) | 87% (26/30) | 19% (12/63) | |
| SPAdes (++rr) | 97% (20/23) | 81% (25/31) | 16% (9/57) | |
| IDBA | 90% (9/10) | 77% (24/31) | 9% (14/149) | |
| REAPR | Velvet | 55% (6/11) | 11% (4/36) | < 1% (2/312) |
| SOAPdenovo | 20% (2/10) | 14% (5/35) | 2% (6/263) | |
| ABySS | 13% (8/64) | 13% (4/32) | 4% (1/23) | |
| SPAdes (−rr) | 27% (3/11) | 27% (8/30) | 5% (3/63) | |
| SPAdes (++rr) | 0% (0/23) | 19% (6/31) | 11% (6/57) | |
| IDBA | 40% (4/10) | 13% (4/31) | 4% (6/149) | |
| Pilon | Velvet | 27% (3/11) | 3% (1/36) | < 1% (3/312) |
| SOAPdenovo | 10% (1/10) | 9% (3/35) | 2% (5/263) | |
| ABySS | 3% (2/64) | 6% (2/32) | 4% (3/23) | |
| SPAdes (−rr) | 0% (0/11) | 3% (1/30) | 5% (5/63) | |
| SPAdes (++rr) | 0% (0/23) | 10% (3/31) | 12% (7/57) | |
| IDBA | 0% (0/10) | 10% (3/31) | 4% (5/149) |
The TPR in this context is a contig that is misassembled and is predicted to be so. The FPR is a correctly assembled contig that was predicted to be misassembled. The TPR and FPR are given as percentages with the raw values given in brackets. Bold values emphasize the benefit of using both data sources.