Fast-track rapid genomics performance. Analytical performances of SNVs and indel detection in nanopore sequencing data. Recall (fraction of true variant detected by nanopore sequencing) and specificity (fraction of variant detected on nanopore data present in the truth set) are calculated over variants binned by read depth at their respective locus on nanopore data. Variants called on WES data were used as ground truth. (A) (Recall): For SNV detection, recall reached a plateau at a sequencing depth of 20×, indicating optimal recall was achieved at this depth. For indels, recall showed more variability but stabilized at a similar depth. (B) (Specificity): Specificity for SNVs and indels plateaued at ∼40× depth, indicating optimal detection beyond this depth. Variants located in regions susceptible to sequencing artifacts, including ENCODE blacklist regions19 and HLA genes, have been excluded. Five patients presenting an outlier number of discordant variants (fourfold greater than the mean of the cohort) were removed from this analysis. SNV, single nucleotide variant.
