Table 3.

F ₁ score, R-squared values and number of predicted genera. For all three analysed mock communities, we inserted the F₁ score (twice the ratio between the product of recall and precision and their sum), the R² value of the linear fit performed between estimated and true abundances together with the number of predicted genera, , with various taxonomic methods. The true number of genera is G = 7 for each community

		Mock 1 (G = 7)			Mock 2 (G = 7)			Mock 3 (G = 7)
		F 1 score	R 2		F 1 score	R 2		F 1 score	R 2
Shotgun	Core-Kaiju	0.92	0.97	6	0.92	0.96	6	0.92	0.71	6
	Standard Kaiju	0.02	0.97	674	0.03	0.98	501	0.02	0.94	738
	MetaPhlAn2	0.86	0.46	7	0.86	0.60	7	0.86	0.08	7
	Kraken2	0.04	0.98	333	0.05	0.99	266	0.04	0.96	378
16S	DADA2 + SILVA	0.48	0.59	18	0.41	0.73	22	0.6	0.41	13
	DADA2 + GG	0.5	0.45	17	0.43	0.60	21	0.63	0.35	12
	DADA2 + RDP	0.48	0.59	18	0.4	0.73	23	0.6	0.41	13
	QIIME2 + SILVA	0.21	0.50	41	0.21	0.59	41	0.21	0.43	41
	QIIME2 + GG	0.26	0.46	32	0.26	0.50	32	0.25	0.36	33