- [MetaPhlAn] - [Python, v4.1.1, 2024.05] - [2023.02, Nat Biotechnoll] - [Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.]
- [StrainPhlAn] - [Python, v4.1.1, 2024.05] - [2017.02, Genome Res] - [Microbial strain-level population structure and genetic diversity from metagenomes.]
- [kraken2] - [C++, v2.1.3, 2023.06] - [2019.11, Genome Biol] - [Improved metagenomic analysis with Kraken 2.]
- [Metabuli] - [C++, v1.0.7, 2024.9] - [2024.05, Nat Methods] - [Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA.]
- [SingleM Microbial Fraction(SMF)] - [Python, na, na] - [2024.09, ISME C] - [Quantifying microbial DNA in metagenomes improves microbial trait estimation.]
- [sylph] - [Rust, v0.6.1, 2024.4] - [2024.1, bioRxiv] - [Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph] - [sylph] - [Rust, v0.6.1, 2024.4] - [2024.10, Nat Biotechnol] - [Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph]
- [Kaiju] - [C, v1.10.1, 2024.3] - [2016.4, Nat Commun] - [Fast and sensitive taxonomic classification for metagenomics with Kaiju.]
- [mOTUs-db] - [web online] - [2024.11, Nuclei Acids Res] - [The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities.]
- [mOTUs] - Reference genome-independent taxonomic profiling of microbiomes with mOTUs3.
- [melon] - [Python, v0.2.4, 2024.12] - [Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes.]
- [kun-peng] - [Rust, v0.7.4, 2024.9] - [2024.12, bioRxiv] - [Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all]
- [MEGAN6] - [2018.4, Biol Direct] - [MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.] [MMseq2/easy-taxonomy] - [C/C++, v15-6f452, 2023.10] - [2021.3, Bioinformatics] - [Fast and sensitive taxonomic assignment to metagenomic contigs.]
- [CDKAM] - [C++/Perl, v1.1, 2020.11] - [2020.10, BMC Bioinformatics] - [CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies.]
- MetaMaps - [Perl/C++, No ver release] - [2019.7, Nat Commun] - [Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.]
- [BugSeq] - [Web Online, 可试用] - [2021.3, BMC Bioinformatics] - [BugSeq: a highly accurate cloud platform for long-read metagenomic analyses.]
- [Vamb/Taxometer] - [Python, v4.1.3, 2023.6] - [2024.9, Nat Commun] - [Taxometer: Improving taxonomic classification of metagenomics contigs]
- [geNomad] - [Python, v1.8.0, 2024.4] - [2023.9, Nat Biotechnol] - [Identification of mobile genetic elements with geNomad.]
-
[GTDB-Tk] - [Python, v1.7.0, 2021.10] - [2020.3, Bioinformatics] - [GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.]
-
[GTDB-Tk 2] - [Python, v2.4.0, 2024.04] - [2022.10, Bioinformatics] - [GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database.]
-
[tronko] - [C, No release] - [2024.9, eLife] - [A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.]
-
[kMetaShot] - [Python, NoReleaseYet, 2024.9] - [2025.1, Briefings in Bioinformatics] - [kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.]