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vdjtools

vdjtools — immune-repertoire analysis

PyPI CI docs python license

TCR/BCR immune-repertoire analysis — a clean-room Python + C++ rewrite of the legacy Groovy/Java vdjtools, standardised on the AIRR schema and polars DataFrames with minimal object-orientation.

Built on the antigenomics ecosystem: seqtree (fuzzy search / e-value engine), vdjmatch (overlap + TCRnet), arda (AIRR annotation + markup repair).

Status: v2.0.0 under active development. The legacy v1.x tool lives on the legacy-1.x branch and its releases remain available under the repository tags (v0.0.1 … 1.2.1).

Install

pip install vdjtools

Prebuilt wheels ship for CPython 3.10–3.13 on Linux, macOS (Apple Silicon), and Windows; the native _core C++ extension is bundled (the source distribution compiles it on install). The pure-analytics paths (diversity / spectratype / usage / overlap) work out of the box; the model and annotation paths additionally pull in arda (MMseqs2):

pip install "vdjtools[model]"

Development

conda env create -f environment.yml   # python + mmseqs2 (arda backend) + C++ toolchain
conda activate vdjtools
pip install -e ".[dev,test]"          # builds the _core C++ extension

Or run the bootstrap script: bash setup.sh --dev-parents --tests.

Capabilities (rolling out by phase — see ROADMAP.md)

  • Model — native V(D)J recombination model: generation probability (Pgen), sequence generation, and EM model inference. Supersedes OLGA and IGoR: arda-driven scenario enumeration, polars marginal tables, D-D tandem support, and a native (pybind11) Pgen/EM core.
  • Stats — diversity (Chao1/Shannon/Simpson/…), spectratype, V/J/VJ usage.
  • Features — CDR physicochemical profiles, k-mer / V+k-mer summaries.
  • Overlap — sample overlap and TCRnet (via vdjmatch/seqtree).
  • Preprocess — downsampling, error-correction, VJ-usage batch-effect correction, pooling/joining.
  • Biomarker — incidence-based association (Fisher) vs HLA / condition / chain-pairing; metaclonotypes.
  • Single-cell — AIRR Cell / 10x interoperability.

License

GPL-3.0-or-later.

Project links

Data verified by PyPI on Jul 11, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

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  • Released:
Newer release available (3.10.0)

1 maintainer

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Avatar for mikessh from gravatar.com mikessh

Credits

Author: Mikhail Shugay

GitHub Statistics

Data verified by PyPI on Jul 11, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

GNU General Public License v3 or later (GPLv3+) (GPL-3.0-or-later)

Requires

Python >=3.10

Provides Extra

model overlap preprocess sc cli examples oracle test bench docs dev all

Tags

immunology tcr bcr airr repertoire pgen olga igor bioinformatics

Classifiers

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