Table 1 Used DMCs to benchmark the classifiers.

Name	Source	Catalog	Chemistry version	Composition	Distribution	Link	Run accession	DMC identifier
Zymo D6300	Zymo Research	D6300	R9	8 bacteria; 2 fungi	Even	https://doi.org/10.1093/gigascience/giz043⁷¹	ERR2906227⁷²	Zymo_D6300
Zymo D6310	Zymo Research	D6310	R9	8 bacteria; 2 fungi	Log	https://doi.org/10.1093/gigascience/giz043⁷¹	ERR2906229⁷³	Zymo_D6310
Zymo D6322	Zymo Research	D6322	R9	7 bacteria 1 fungus	Even, except the fungus	https://doi.org/10.1038/s41592-022-01539-7⁷⁴	ERR7255742⁷⁵	Zymo_D6322
Zymo D6322	Zymo Research	D6322	R10	7 bacteria 1 fungus	Even, except the fungus	https://doi.org/10.1038/s41592-022-01539-7⁷⁴	ERR7287988⁷⁶	Zymo_D6322_r10
Zymo D6331	Zymo Research	D6331	R9	1 archaea; 14 bacteria; 2 fungi	Staggered	https://doi.org/10.1186/s40168-022-01415-8¹⁷	SRR17913200⁷⁷	Zymo_D6331
Bei Resources HM-276D	Bei Resources	HM-276D	R9	20 bacteria	Even	https://doi.org/10.1016/j.isci.2020.101223⁷⁸	SRR11700265⁷⁹	BeiRes_276D
Bei Resources HM-277D	Bei Resources	HM-277D	R9	20 bacteria	Staggered	https://doi.org/10.1016/j.isci.2020.101223⁷⁸	SRR11700264⁸⁰	BeiRes_277D
Strain madness 1	Meslier, V., Quinquis, B., Da Silva, K. et al.	/	R9	22 archaea; 45 bacteria	Staggered	https://doi.org/10.1038/s41597-022-01762-z⁸¹	ERR9765780⁸²	StrainMad_1
Strain madness 2			R9	22 archaea; 61 bacteria			ERR9765781⁸³	StrainMad_2
Strain madness 3			R9	14 archaea; 46 bacteria			ERR9765782⁸⁴	StrainMad_3

The first column contains the dataset names. The second and third columns give the origin and catalog number (if applicable). The fourth column shows the nanopore chemistry used for sequencing. The fifth and sixth columns provide information on the composition of each dataset. The seventh column refers to the DOI number from where the datasets originate. The eighth column refers to the run accession number of the sequencing data. The last column is used a reference key to the DMCs throughout the text and figures. More detailed information on the exact composition of the DMCs, including their relative abundances, is available in Supplementary Table S3.
Abbreviations: DMC: Defined Mock Community; DOI: Digital Object Identifier.

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