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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)

From: Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

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 %