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Table 1 Accuracy metrics for different de novo and reference-based mitochondrial genome assemblies using nanopore long reads exclusively in the silky shark Carcharhinus falciformis

From: Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis

Assembly Pipeline Contigs Length Coverage p-dist Errorsb
Flye +1p circular 16,690 20x 0.001023172 65
Flye +1p + Medaka circular 16,475 20x 0.000541679 70
Flye +5p circular 16,691 20x 0.001023172 69
Flye +5p + Medaka circular 16,475 20x 0.000541679 71
Flye +10p circular 16,691 20x 0.001023172 69
Flye +10p + Medaka circular 16,475 20x 0.000541679 71
Unicycler - N circular 16,801 2.28xa 0.001143545 110
Unicycler - N + Medaka circular 16,781 2.28xa 0.000601866 89
Unicycler - B circular 16,801 2.28xa 0.001143545 110
Unicycler - B + Medaka circular 16,781 2.28xa 0.000601866 89
Unicycler - C circular 16,801 2.28xa 0.001143545 110
Unicycler - C + Medaka circular 16,781 2.28xa 0.000601866 89
Rebaler - P. amblyrhynchos circular 15,782 50.59x 0.001324105 106
Rebaler - P. ambly. + Medaka circular 16,774 50.59x 0.000541679 81
Rebaler - P. amboinensis circular 15,790 49.94x 0.000902799 95
Rebaler - P. ambo. + Medaka circular 16,776 49.94x 0.000361119 73
Rebaler - P. falciformis circular 16,789 52.52x 0.000842612 96
Rebaler - P. falci. + Medaka circular 16,777 52.52x 0.000541679 81
Reference mtDNA circular 16,705 9.8x
  1. aUnicycler normalizes the depth of contigs to the median value
  2. bError refers to total number of errors quantified in the long-read assemblies compared to the short read assembly. Errors were classified as single, double, triple, quadruple, quintuple, sextuple, or septuple “homopolymer insertions’ or ‘homopolymer deletions’, ‘simple substitution’, ‘single insertion’, ‘short insertion (< 5 bp)’, ‘single deletion’, and ‘short deletion (< 5 pb)’