Table 1.
Comparison of SENSV, NanoVar, Sniffles, SVIM and cuteSV on the ability to detect the pathogenic SV from the 24 patients’ ONT WGS data.
| ID | SV length | SV type | Detect the pathogenic SV? (# of predicted SVs of the same type) | ||||
|---|---|---|---|---|---|---|---|
| SENSV | NanoVar | Sniffles | SVIM | cuteSV | |||
| Difficult cases | |||||||
| 1 | 146 K | Long deletion | Y (1513) | Y (1278) | Y- (1027) | Y (2078) | Y (831) |
| 2 | 266 K | Long deletion | Y (1431) | Y (1353) | Y (1172) | Y (2129) | Y (945) |
| 3 | 638 K | Long deletion | N (1743) | N (1146) | N (732) | N (2207) | N (599) |
| 4 | 670 K | Long deletion | Y (1612) | N (1176) | N (794) | N (2036) | N (658) |
| 5 | 1.5 M | Long deletion | Y (3395) | N (1514) | N (1062) | N (4970) | N (848) |
| 6 | 1.4 M | Long deletion | Y (17,209) | N (3692) | N (1375) | Y- (17,783) | N (834) |
| 7 | 1.4 M | Duplication | Y (200) | N (1779) | N (667) | Y- (1901) | N (2105) |
| 8 | 2.8 M | Long deletion | Y (1,792) | N (1320) | N (1192) | N (2983) | N (1016) |
| 9 | 5.2 M | Long deletion | Y (1515) | N (1294) | N (1014) | N (1982) | N (786) |
| 10 | 6.6 M | Long deletion | Y (2868) | N (1474) | Y (1362) | Y (4534) | Y (1090) |
| 11 | 342 K | Unbalanced translocation | N (490) | N (7106) | N (1383) | N (1154) | N (1310) |
| 12 | 1.4 M | Unbalanced translocation | Y (462) | N (7802) | N (1432) | N (1179) | N (1326) |
| 13* | 5.9 M | Terminal deletion | Y (3476) | N (1498) | N (1510) | N (4649) | N (1168) |
| 14 | 18 M | Unbalanced translocation | Y (269) | N (6156) | N (1719) | N (1429) | N (1595) |
| 15 | 19 M | Terminal deletion | Y (1413) | N (1220) | N (968) | N (2031) | N (798) |
| 16 | 58 M | Unbalanced translocation | Y (883) | N (6688) | N (2340) | N (2053) | N (2263) |
| Others | |||||||
| 17 | 142 K | Inversion | Y (114) | Y- (1413) | Y- (1391) | Y- (849) | Y (1336) |
| 18* | 73 M | Inversion | Y (118) | Y (1333) | Y (853) | Y (523) | Y- (903) |
| 19 | 33 M | Inversion | Y (192) | Y (1258) | N (190) | Y (117) | N (210) |
| 20 | N/A | Balanced translocation | Y (89) | Y (5554) | Y (1463) | Y (1190) | Y (1404) |
| 21* | N/A | Balanced translocation | Y (861) | Y (6898) | Y (2594) | N (2012) | Y (2518) |
| 22 | N/A | Balanced translocation | Y (76) | Y (5254) | Y (1187) | N (996) | Y (1084) |
| 23 | N/A | Balanced translocation | Y (111) | Y (5542) | Y (1449) | N (1065) | Y (1319) |
| 24 | N/A | Balanced translocation | Y (592) | Y (6628) | Y (1775) | Y (1358) | Y (1645) |
Below, “Y” [and “Y-”] mean that a method can detect the pathogenic SV with correct SV type and with breakpoints off by at most 100 bp [and by at most 2000 bp respectively]; and “N” indicates the method unable to detect the SV with breakpoints off by at most 2000 bp. SENSV can detect more SVs, especially for difficult cases, with much fewer false positives. Other software usually detects much more SVs than SENSV but most of them are false positives. The samples ID with asterisk have been basecalled using both Guppy versions (v3.1.5 and v5.0.11).
The best results of a row are in bold.