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Table 2 Classification of 474,930,848 simulated sequencing reads (low substitution rate) by Kraken, Kraken2, the MEM approaches Kaiju and PRROMenade compared to alignment using Bowtie2 and DIAMOND. Analysis conducted using the full IFGP GO term sequence database and functional annotation

From: Re-purposing software for functional characterization of the microbiome

Software

Speed (user time + system time in seconds)

Peak memory (GB)

% Classified/aligned reads

Parameters

Diamond (MEGAN/mi-faser/HUMAnN2)

9,791,017

21.61

98.82

-k 1

Bowtie2 (HUMAnN2)

758,766

58.26

92.95

-S (output SAM file)

Kaiju

456,225

16.44

85.14

-a mem

PRROMenade

219,483

140.38

85.14

taxonomic-classifierMem

Kraken

23,220

35.2

85.20

Defaults

Kraken 2

9466

1.95

93.91

Defaults