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

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

Assembly Pipeline	Contigs	Length	Coverage	p-dist	Errors^b
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	2.28x^a	0.001143545	110
Unicycler - N + Medaka	circular	16,781	2.28x^a	0.000601866	89
Unicycler - B	circular	16,801	2.28x^a	0.001143545	110
Unicycler - B + Medaka	circular	16,781	2.28x^a	0.000601866	89
Unicycler - C	circular	16,801	2.28x^a	0.001143545	110
Unicycler - C + Medaka	circular	16,781	2.28x^a	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	–	–

^aUnicycler normalizes the depth of contigs to the median value
^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)’

ISSN: 1471-2164