TABLE 2.
Tools and databases available for phylogenetic identification
| Phylogenetic identification tool/database | Version used for this review | Database type | Target collection(s) | Database size (Gb) | Yr of latest update | Time required to build database at first use (h) | Time required to generate classification resultsa | Reference |
|---|---|---|---|---|---|---|---|---|
| Kraken2 | v2.0.8-beta | DNA | RefSeq bacteria | 103 | 2019 | 15 | 3 min | 66 |
| MiniKraken2 | v2 | DNA | RefSeq bacteria, archaea, viruses, GRCh38 human genome data set | 8 | 2019 | Not required | 2 min | 66 |
| Kaiju | v1.7.2 | Protein | Eukaryotes, bacteria, viral genomes | 97 | 2019 | 4 | 2 h | 67 |
| MetaPhlAn2 | 0c3ed7b7718b | Marker gene | Eukaryotes, bacteria, archaea, viruses | 1 | 2018 | Not required | 2 h | 68 |
| mOTUs2 | v2.5.1 | Marker gene | Eukaryotes, bacteria, archaea | 1.5 | 2018 | Not required | 40 min | 69 |
a
Denotes the time required to generate the classification results from a test data set generated from Illumina HiSeq 4000 paired-end sequencing. The data set contains approximately 7 million trimmed paired reads of an average of 150 bp, with a 600-Mb fastq.gz file.