Intended Use | Method | Variations | Reference database | Strategy |
---|---|---|---|---|
Short reads | Kraken2 | – | “PlusPF” | K-mer-based |
Bracken | – | “PlusPF” | Bayesian Refinement | |
Centrifuge | h22, h500 | Refseq ABVF | BW transform, FM-index | |
MetaPhlAn3 | – | mpa_v30_CHOCOPhlAn_201901 | Read mapping, coverage scores | |
mOTUs2 | – | V3.0.3 | Read mapping | |
General | sourmash | k31, k51 | GenBank | K-mer min-set-cov; LCA algorithm |
Long reads | MetaMaps | – | MiniSeq + H | Approximate mapping |
MMseqs2 | – | NCBI nr | Translation alignment, LCA algorithm | |
MEGAN-LR-prot | – | NCBI nr | Translation alignment, LCA algorithm | |
MEGAN-LR-nuc | HiFi, ONT | NCBI nt | Nucleotide alignment, LCA algorithm | |
BugSeq-V2 | – | NCBI nt | Nucleotide alignment, LCA algorithm |