Skip to main content

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