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Fig. 2 | Genome Biology

Fig. 2

From: NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing

Fig. 2

NanoVar performance benchmarking. a, b SV breakend precision and recall by SV caller tools in simulation data with homozygous or heterozygous SVs. There are three homozygous SV datasets with 42,000 SVs each and one heterozygous SV dataset with 42,000 SVs at different sequencing depths. For tools with SV scoring, the optimal score was selected for them based on the F1 score at 4X sequencing depth (NanoVar, 1.0; NanoSV, 0; SVIM, 0; novoBreak, 27.5). The markers of different tools are separated by color, while different sequencing depths are separated by shapes. b, c Radar charts showing the F1 scores for each SV class characterized by each tool for homozygous and heterozygous SVs in simulation 1. DUP tandem duplication, DEL deletion, INS insertion, BND breakend, INV inversion. We presented the tools separately according to their utilization of 3GS and 2GS data. SV class annotation evaluation was included in this analysis. e, f Recall of homozygous and heterozygous SVs intersecting with SINE and LINE regions as detected by the different tools. The tools are separated by the same color code as the other plots in this figure. SV analysis of the other repetitive sequence families can be found in Additional file 1: Fig. S3

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