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Vamb

Read the Docs

Vamb is a metagenomic binner which feeds sequence composition from a FASTA file of contigs, and abundance information from e.g. BAM files into a variational autoencoder and clusters the latent representation. It performs excellently with multiple samples, and pretty good on single-sample data.

  • New: For benchmarking binnings with a known ground truth, see our tool BinBencher.jl
  • New: The new semi-supervised TaxVamb binning mode achieves state-of-the-art binning

Programs in Vamb

The Vamb package contains several programs, including three binners:

  • Vamb: The original binner based on variational autoencoders. Article. This has been upgraded significantly since its original release.
  • Avamb: An ensemble model based on Vamb and adversarial autoencoders. Article. Avamb produces better bins than Vamb, but is a more complex and computationally demanding pipeline. See the Avamb README page for more information.
  • TaxVamb: A semi-supervised binner that uses taxonomy information from e.g. mmseqs taxonomy. Article. TaxVamb produces superior bins, but requires you have run a taxonomic annotation workflow.

And a taxonomy predictor:

  • Taxometer: This tool refines arbitrary taxonomy predictions (e.g. from mmseqs taxonomy) using kmer composition and co-abundance. Go to the release branch for the instructions. Article

See also our tool BinBencher.jl for evaluating metagenomic bins when a ground truth is available, e.g. for simulated data or a mock microbiome.

Installation

Vamb is in continuous development. Make sure to install the latest version for the best results.

Installation for casual users:

Recommended: Vamb can be installed with pip (thanks to contribution from C. Titus Brown):

pip install vamb

Note: An active Conda environment can hijack your system's linker, causing an error during installation. Either deactivate conda, or delete the ~/miniconda/compiler_compats directory before installing with pip.

Installation for advanced users:

If you want to install the latest version from GitHub, or you want to change Vamb's source code, you should install it like this:

# clone the desired branch from the repository, here master
git clone https://github.com/RasmussenLab/vamb -b master
cd vamb
pip install -e .

Note that the master branch is work-in-progress and is expected to have more bugs

Installing by compiling the Cython yourself

If you can't/don't want to use pip/Conda, you can do it the hard way: Install the dependencies listed in the pyproject.toml file. Compile src/_vambtools.pyx then move the resulting binary to the inner of the two vamb directories. Check if it works by importing vamb in a Python session.

Running Vamb

First, figure out what program you want to run:

  • If you want to bin, and are able to get taxonomic information, run vamb bin taxvamb
  • Otherwise, if you want a good and simple binner, run vamb bin default
  • If you want to bin, and don't mind a more complex, but performant workflow run the Avamb Snakemake workflow
  • If you want to refine existing taxonomic classification, run vamb taxometer

For more command-line options, see the command-line help menu:

vamb -h

For details about how to run Vamb, see the documentation