Table 2 Scores of the assemblies generated by each mitochondrial genome assembler for samples with a mean sequencing depth of 10X

Sr. no.	Assembler	Median	IQR	Perfect assemblies
1	ARC	28.85	7.20	0
2	GetOrganelle	99.99	0.01	6
3	IOGA	99.98	0.03	6
4	MEANGS	99.97	0.19	5
5	MITObim	0	0.00	0
6	MitoFlex	99.99	0.001	6
7	MitoZ	99.97	1.58	4
8	MToolBox	100.00	0.00	6
9	NOVOPlasty	99.99	0.01	6
10	ORG.Asm	99.99	0.03	6

Overall GetOrganelle, IOGA, MitoFlex, MToolBox, NOVOPlasty and ORG.Asm produced the perfect assemblies (score > 99) for all six datasets, followed by MEANGS and MitoZ. MITObim and ARC failed to produce good-quality assemblies for these datasets. Information about the scores obtained for the original, 40X and 20X sequencing data assemblies is available in the Additional file 2: Table S4

ISSN: 1471-2105