📚 Tools and databases for analyzing HLA and VDJ genes.
immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene families. It supports both WGS and amplicon data. It supports PacBio and Nanopore data.
Standardise TR/MH/IG data
BASIC: BCR and TCR assembly from single cell RNA-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.
Substitution Profiles Using Related Families
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.
Machine learning for Immune Repertoires
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A three-part R tutorial for single-cell BCR sequence processing and integration with gene expression data, using Immcantation and Seurat
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).
An implementation of Byzantine Chain Replication for Distributed Systems
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