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 |