vdjmatch — TCR peptide–MHC annotation
vdjmatch annotates selected T-cell receptors and repertoires against
VDJdb, preserving query identities and
reporting peptide–MHC candidates, competing evidence and optional background calibration.
Native sequence search uses seqtree;
repertoire ingestion reuses published vdjtools readers.
Requires released seqtree>=1.3.2 and vdjtools>=5.6.0, including allocation-aware
native thread validation.
Quick start
python -m pip install vdjmatch
vdjmatch annotate sample.tsv --threads 4 -o annotation
Use AIRR junction_aa (including conserved anchors) and V calls. The curated
VDJdb reference is fetched on first use; add --vdjdb reference.zip for offline
input. Single TRA/TRB receptors and paired receptors are supported. Exact hits
are retained by default. Scores describe sequence evidence, not proof of binding.
For a small offline example, download the examples directory and run
sh examples/annotate.sh annotation-demo from the repository root.
Documentation
| Need | Guide |
|---|---|
| Learn the workflow | Getting started · Rendered notebooks |
| Annotate a cohort or use an offline reference | How-to guides · Runnable examples |
| Look up inputs, options and outputs | CLI reference · Python API |
| Understand methods and formulas | Scoring · Evidence and calibration |
| Test repertoire enrichment | Matching, nulls and count units |
| Estimate precursor frequency | Method · Experimental compendium |
The legacy Java/Groovy implementation remains on legacy-java
and Java tag 1.3.1, with
JitPack artifact com.github.antigenomics:vdjmatch:1.3.1.
License
ISALGO LAB Academic and Non-Commercial Research License v1.0. See LICENSE.
1 maintainer
Metadata
1 maintainer
Release files for vdjmatch 1.2.0
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