Table 1 Comparison of taxonomic classifiers: performance metrics, database composition and classification accuracy
From: An in-depth evaluation of metagenomic classifiers for soil microbiomes
Classifier | MetaPhlAn | Kraken2 and Bracken | Kaiju | ||
|---|---|---|---|---|---|
Version | MetaPhlAn3 v.30 | MetaPhlAn4 v.4.0 | Kraken2/2.1.1 and Bracken/2.2 | Kaiju/1.7.4 | |
Database | CHOCOPhlAn 201901 | CHOCOPhlAnSGB 202103 | plus-pf | custom database | nr-euk |
Organisms included in the database | Bacteria, Archaea, Eukaryota | Bacteria,Archaea, *Microbial Eukaryotes, *Virus | Bacteria, Archaea, Eukaryota, plasmid, human, Univec_core, Protozoa | Bacteria, Archaea, Eukaryota | Bacteria, Archaea, Eukaryota, Virus, Microbial Eukaryotes |
Database size | 2.4 GB | 23 GB | 61 GB | 1.2 TB | 144 GB |
Processing time per sample (h:m:s) | 3:02:38 | 4:24:14 | 0:43:29 | 2:20:08 | 11:23:26 |
Species F1 score (optimal threshold) | 0.26 ± 0.02 | 0.41 ± 0.02 | 0.74 ± 0.01 | 0.68 ± 0.0 | 0.48 ± 0.01 |
Species F1 score (no threshold) | 0.26 ± 0.02 | 0.42 ± 0.02 | 0.5 ± 0.01 | 0.63 ± 0.01 | 0.11 ± 0.01 |
Unclassified | 94.5% | 90.6% | 79.3% | 0.46% | 37.43% |
Classified | 5.5% | 9.4% | 20.7% | 99.54% | 62.57% |