Table 2.

Mapping summary per mock and sequencing technology.

Sample ID	Sequencing Technology	N. reads before trimming (million)	N. reads after trimming (million)	%Mapped end-to-end	%Uniquely mapped	%Avg end-to-end best mapped identity	%Avg end-to-end best mapped substitutions	%Avg end-to-end best mapped in/dels
MOCK1 (N = 71 species)	Illumina HiSeq 3000	21.38*2	20.59*2	99.62	93.21	99.45	0.46	0.09
	Ion Proton P1	21.23	20.00	99.29	87.13	99.42	0.12	0.46
	Ion S5	30.05	28.51	99.35	87.13	99.61	0.08	0.31
	ONT Minion R9	0.757	0.696	99.75	99.63	89.08	3.37	7.55
	PacBio Sequel II	0.525	0.524	99.65	99.62	99.72	0.06	0.22
	DNBSEQ-G400	36.17*2	35.42*2	99.22	89.16	99.70	0.30	0.003
	DNBSEQ-T7	404.06*2	375.12*2	98.92	88.78	99.42	0.58	0.003
MOCK2 (N = 87 species)	Illumina HiSeq 3000	24.27*2	23.17*2	99.66	89.44	99.43	0.49	0.08
	Ion Proton P1	22.21	20.98	99.46	86.61	99.41	0.12	0.47
	Ion S5	25.36	24.17	99.55	86.66	99.59	0.09	0.32
	ONT Minion R9	0.919	0.831	99.74	99.61	89.05	3.39	7.56
	DNBSEQ-G400	37.92*2	37.14*2	99.43	88.85	99.73	0.27	0.003
	DNBSEQ-T7	404.99*2	376.04*2	99.03	88.32	99.46	0.54	0.003
MOCK3 (N = 64 species)	Illumina HiSeq 3000	63.97*2	62.08*2	99.58	90.36	99.39	0.52	0.09
	Ion Proton P1	21.50	20.26	99.15	88.33	99.44	0.11	0.45
	Ion S5	27.32	25.90	99.31	88.40	99.62	0.08	0.30
	ONT Minion R9	0.865	0.791	99.79	99.61	89.06	3.35	7.59

The number of reads before and after trimming refer to the sequencing depth (million reads) before and after quality control filtering and trimming. %Mapped end-to-end correspond to the read percentage aligned to a reference genome considering the read full length, while %Uniquely mapped reads correspond to the percentage of reads aligned to only one region of a reference genome. %Avg end-to-end refer to the best hit mean percentage for mapped identity and substitutions and insertions/deletions (in/dels) respectively. See the Method section for trimming and mapping parameters.