airr-seq

Fast simulator of BCR and TCR sequences with full ground-truth annotations: V(D)J recombination, somatic hypermutation and sequencing artifacts across 23 species. Rust core with a Python API, for training and benchmarking AIRR-seq tools.

Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

TCRscape - a tool for simultaneous multimodal gene expression and clonotype analysis of single T-cells profiled via the BD Rhapsody system.

Deep-learning V(D)J aligner for BCR and TCR sequences. A single model predicts V/D/J allele calls, segment boundaries and the junction, with AIRR-format output. Published in Nucleic Acids Research (2025).

Extract TCR and BCR clonotypes from raw sequencing data. Alignment against germline gene databases, error correction, receptor assembly, and clonotype grouping — turning FASTQ into a quantified repertoire with full QC.

Quality control scripts for AIRR-seq data

Barbera van Schaik, Antoine van Kampen: ENCORE project for analysis for T-cell and B-cell repertoires

Explore and annotate your sequences interactively, lets you write rule-based annotations that tag sequences by any criteria you choose

Barbera van Schaik, Antoine van Kampen: REpertoire SEquence Data Analysis

Matches clonotypes between two V(D)J datasets — typically a deep bulk dataset and a smaller single-cell reference — so any property from the reference becomes available on the matched bulk clonotypes.

A zero-dependency C++ wrapper for NCBI IgBLAST. Embeds IMGT databases and binaries into a single executable for standalone V(D)J assignment and enriched AIRR-formatted outputs.

VBASE3: Unified Comparative Immunogenomics Database, Synthesis-Ready Germline Catalog Across 53 Vertebrate Species, and WebAssembly Analytics Suite

Demultiplexing pipeline for Kinnex HiFi TCR/BCR-seq

Rodrigo Garcia Valiente: Visual artsy representation of B-cell clonal repertoires using R

This repository contains bioinformatics workflows and Jupyter notebooks developed by the Molecular Virology and Vaccines Team (MVVT) for adaptive immune receptor repertoire sequencing (AIRR-seq) data. The workflows support B-cell receptor (BCR) repertoire analysis from bulk and single-cell sequencing data.

Probability model for biological sequences such as TCRβ CDR3s, learned from sequences alone with optional abundances: sequence probabilities, sequencing depth, publicness and repertoire comparison, summed over every combinatorially possible sequence without enumeration or simulation.

Calculates V and J gene segment usage frequencies across samples, plus their pairwise combinations, revealing the germline biases that antigen exposure, vaccination, and disease leave behind.

Re-groups an existing V(D)J dataset by a definition you choose — any combination of V gene, J gene, and CDR3 sequence — picks a representative for each new group, and recalculates every abundance column by summing across the members.

Immunogenomics benchmark + skillset for AI agents