Table 1.

Benchmarking of taxonomic assignment tasks using simulated reads (ICTV and HIV-1)

Datasets	Simulated reads (50 bp, n = 1million) from ICTV standard genomes		Simulated reads (150 bp, n = 100 k) from ICTV standard genomes		Simulated divergent HIV-1 reads (150 bp, n = 100 k) (100 generations)	Simulated divergent HIV-1 reads (150 bp, n = 100 k) (1 K generations)	Simulated divergent HIV-1 reads (150 bp, n = 100 k) (10 K generations)
Metrics	Kappa	F1	Kappa	F1	Prediction accuracy	Prediction accuracy	Prediction accuracy
Kraken 2	0.3139	0.3184	0.7274	0.7318	0.9664	0.7755	4.890 × 10–3
Centrifuge	0.5953	0.6011	0.7219	0.7266	0.8865	0.8679	3.056 × 10–2
Bowtie 2	0.9597	0.9605	0.9991	0.9991	0.9976	0.9828	8.501 × 10–4
MT-CNN	0.9464	0.9475	0.9976	0.9976	1.000	0.9963	0.1531