Table 2.

RNA-seq datasets used to test two automated virus detection tools.

Organism	SRA ID	Data type	Viruses detected in original analysis
Pear (Pyrus pyrifolia)	SRR1269627	RNA-seq, SE	ASGV, AGCAV, ASPV, PrVT (Jo et al., 2016)
Pepper (Capsicum annuum)	SRR1123893	RNA-seq, PE	ALPV, BPEV, cgLCuV, CYVMVA, PepLCB, PepLCBV, PeSV, ToLCRnV, ToLCBDB, ToLCJoV, GaILV, TolCGV, TVCV (Jo et al., 2017)
Grape Vine (Vitis vinifera)	SRR3680863	sRNA-seq, SE	GRSPaV, GVB, GFkV, GLRaV-3, HSVd (Barrero et al., 2017)

The specific sequence datasets used are indicated by their SRR number in the SRA (Leinonen et al., 2011). SE, Single-end; PE, Paired-end.

Pear: Prunus virus T (PrVT), Apple green crinkle associated virus (AGCAV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV). Pepper: Aphid lethal paralysis virus (ALPV), Pepper leaf curl Bangladesh virus (PepLCBV), Pea streak virus (PeSV), Pepper leaf curl virus betasatellite (PepLCVB), Tobacco vein clearing virus (TVCV), Bell pepper endornavirus (BPEV). Tomato leaf curl Ranchi virus (ToLCRnV), Tomato leaf curl Bangladesh betasatellite (ToLCBDB), Tomato leaf curl virus (ToLCJoV), Tomato leaf curl Gujarat virus (TolCGV), Cotton leaf curl virus (CLCuV), Croton yellow vein mosaic virus (CYVMVA), Pepper leaf curl virus betasatellite (PepLCVB), Gaillardia latent virus (GaILV). Grape vine: Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine virus B (GVB), Grapevine fleck virus (GFkV), Grapevine leafroll-associated virus (GLRaV-3), Hop stunt viroid (HSVd).