🦠 Best AI tools for Microbiome & metagenomics (2026)
Metagenomic profiling, binning, MAG quality, taxonomy and virus/plasmid detection.
9 tools · 8 open source · each entry links to its website, code and paper.
Marker-gene-based taxonomic profiling of metagenomes, including uncharacterized species.
Self-supervised deep learning metagenomic binning for short and long reads.
Neural-network and marker-based identification of viruses and plasmids in sequencing data.
Machine-learning estimation of completeness and contamination of metagenome-assembled genomes.
Functional profiling of metagenomes and metatranscriptomes (gene families and pathways).
Extensible platform for microbiome (amplicon and shotgun) data science.
Variational autoencoder for metagenomic binning.
Fast k-mer based taxonomic classification of metagenomic reads.
Assigns GTDB taxonomy to bacterial and archaeal genomes and MAGs.