Table 1.

Processing time of Taxonomer compared to rapid classification pipelines SURPI and Kraken. RNA-Seq data generated from three nasopharyngeal specimens with varying taxonomic composition illustrate differences in analysis times between the three tools. (Human: blue; Bacteria: orange; Fungal: green; Virus: red; Other: yellow; Unclassified: gray)

Sample composition, total reads	Pathogen	Application	Subtraction	Binning	Classification	Protein search	Total time	% Reads classified
6,599,164	HCoV	Taxonomer	-	5 min	22 s	10 s	5.5 min	99.9 %
		Kraken	-	-	1.5 min	-	1.5 min	99.6 %
		SURPI	3.3 min	-	74 min	15 min	92 min	99.9 %
7,542,552	Influenza A virus	Taxonomer	-	8 min	40 s	30 s	9.2 min	88 %
		Kraken	-	-	1.5 min	-	1.5 min	66 %
		SURPI	9.8 min	-	208 min	18 min	236 min	78 %
6,252,311	HMPV	Taxonomer	-	5.2 min	56 s	10 s	6.3 min	98 %
		Kraken	-	-	1.3 min	-	1.3 min	93 %
		SURPI	56 min	-	648 min	24 min	728 min	95 %