Table 2 Comparison of virus and viroid detection with different pipelines
From: PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data
Expected viruses and viroids | Challenge | PhytoPipe | Kodojaa | Pathoscopeb | Virtool | |||||
|---|---|---|---|---|---|---|---|---|---|---|
Detection (detected/all) | Challenge finish status | Detection (detected/all) | Challenge finish status | Detection (detected/all) | Challenge finish status | Detection (detected/all) | Challenge finish status | |||
Dataset_1 | CTV, CVEV, CEVd, CVd-III, HSVd | Different viral concentration (CTV) | 5/5 | Found different CTV strains | 2/5 (CEVd, CVd-III, HSVd missed) | Not applicable | 5/5 | Not applicable | 5/5 | Not applicable |
Dataset_3 | GRSPaV, GLRaV2, GRVFV, HSVd, GYSVd-1 | Different viral concentration (at the species level) + Non complete virus genome coverage (GRSPaV, GLRaV2 and GRVFV) | 5/5 | Viruses at the species level were found | 3/5 (HSVd, GYSVd-1 missed) | Not applicable | 4/5 (GRVFV missed) | Not applicable | 2/5 (GRSPaV, GRVFV, GYSVd-1 missed) | Viruses with non-complete genome could be missed |
Dataset_4 | GRBV, GRSPaV, HSVd, GYSVd-1, GYSVd-2 | Very similar viroids sequence (GYSVd-1 and GYSVd-2) | 5/5 | Two similar viroids were found | 2/5 (HSVd, GYSVd-1, GYSVd-2 missed) | Not applicable | 5/5 | Not applicable | 4/5 | Can’t separate GYSVd-1 and -2 |
Dataset_5 | PVY NTN and N strains | Mix of recombinant and parental PVY strains | 2/2 | Different PVY strains and recombinants were detected | 1/1 | Not applicable | 1/1 | Not applicable | 1/1 | Recombinant NTN detected, not parental strains |
Dataset_6 | PVY | New PVY strain | 2/2 | New PVY strain detected | 1/1 | Not applicable | 1/1 | Not applicable | 2/2 | New PVY strain detected |
Dataset_7 | TSWV | Complete genome + defective form of TSWV | 2/2 | A defective L segment of TSWV was detected | 1/1 | Not applicable | 1/1 | Not applicable | 2/2 | A defective L segment of TSWV was detected |
Dataset_8 | PFBV, CqMV1 | Cryptic mitovirus virus + low mitovirus concentration | 2/2 | A low concentration CqMV1 was detected | 1/2 (CqMV1 missed) | Not applicable | 2/2 | Not applicable | 1/2 (CqMV1 missed) | Mitovirus missed |
Dataset_9 | PiVB | Concentration of different PiVB genomic segments | 1/1 | All eight PiVB segments were detected | 0/1 (PiVB missed) | Not applicable | 1/1 | Not applicable | 0/1 (PiVB missed) | Not applicable |
Dataset_10 | PBNSPaV, PPV | New PPV strain | 2/2 | New PPV strain was detected | 1/2 (PPV missed) | Not applicable | 1/2 (PPV missed) | Not applicable | 2/2 | New PPV strain was detected |