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Table 1 Functional classification of 474,930,848 simulated (low substitution rate) sequencing reads by Kraken, Kraken 2 and MEM approaches (Kaiju and PRROMenade) using the full IFGP sequence database

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

Software

Database format

% Unclassified reads

% Classified Reads

% Classified reads assigned to the root

% Classified reads assigned to correct GO term or related non-root LCF

% Classified reads assigned to an incorrect GO term

Kraken

DNA

14.80

85.20

14.20

84.10

1.70

Kraken 2

Amino Acid

6.09

93.91

13.71

86.29

1.12

MEM

Amino Acid

14.86

85.14

14.61

84.71

0.68