vdjtools

TCR/BCR immune-repertoire analysis — v2, a clean-room rewrite in Python + C++.

Standardised on the AIRR schema and polars DataFrames with minimal object-orientation, built on the antigenomics ecosystem (seqtree, vdjmatch, arda).

Warning

v2.0.0 is under active development. The legacy Groovy/Java vdjtools (v1.x) lives on the legacy-1.x branch and its releases remain available under the repository’s tags.

Capabilities (rolling out by phase — see the project ROADMAP):

• Model — native V(D)J recombination model: generation-probability (Pgen), sequence generation, and EM model inference (supersedes OLGA and IGoR).

• Stats — diversity, 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, batch-effect correction.

• Biomarker — incidence-based association (Fisher) and metaclonotype grouping.

• Single-cell — AIRR Cell / 10x interoperability.