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Metabuli - Sensitive and Specific Taxonomic Classification

Sensitive and Specific. Metabuli integrates DNA- and amino acid-level searches. It leverages AA conservation for sensitive homology detection and DNA mutations for specific differentiation between closely related taxa.

A laptop is enough. Metabuli operates within user-specified RAM limits, allowing it to search any database that fits in storage. A PC with 8 GiB of RAM is sufficient for most analyses.

A few clicks are enough. Metabuli App is available for Windows, macOS, and Linux. With just a few clicks, you can run Metabuli and browse the results with Sankey and Krona plots on your PC.

Short reads, long reads, and contigs. Metabuli can classify all types of sequences.

Check out [new features] and databases in Metabuli v1.2.0!

🖥️ Metabuli App for Windows, macOS, and Linux

  • Run taxonomic classification and explore results with interactive Sankey and Krona plots.
  • Download the app for your OS. No separate Metabuli installation needed.

Installation

Three easy options:

  1. Install via conda: conda install -c conda-forge -c bioconda metabuli
  2. Download ready-to-use binaries at https://mmseqs.com/metabuli.
    • Linux, macOS, and Windows builds available.
  3. Compile from source 
    git clone --recurse-submodules https://github.com/steineggerlab/Metabuli.git
cd Metabuli
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j

Modules

Module Description
classify Classify metagenomic reads against a reference database
refine-results Refine classification results with additional filtering options
extract Extract reads classified under a specific taxon
build Build a custom reference database
updateDB Add new sequences to an existing database

Publications and Citations

  • Jaebeom Kim and Martin Steinegger. Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA. Nature Methods (2024). Journal, PDF, ISMB 2023 talk
  • SunJae Lee and Jaebeom Kim et al. Easy and interactive taxonomic profiling with Metabuli App. Bioinformatics (2025). Journal
  • Jaebeom Kim and Martin Steinegger. Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers. bioRxiv (2026). Preprint