vdjmatch

TCR specificity and repertoire annotation

From receptor sequences to peptide–MHC evidence. Annotate TRA/TRB receptors, linked pairs or whole repertoires while keeping source identities, competing labels and unsupported queries visible.

Get started· Command line· Examples· Notebooks

Version 0.4.0. Install the published package and annotate your AIRR table:

python -m pip install vdjmatch
vdjmatch annotate sample.tsv --threads 1 -o annotation

The reference is fetched on first use. Choose --vdjdb reference.tsv for an offline run, or start with the tiny synthetic inputs in Examples gallery.

Tutorials

Annotate your first receptors

Install, run a small offline cohort and paired sample, then read the output tables.

How-to guides

Run your own cohort

Choose a reference, prepare AIRR inputs, preserve pairing and set a resource budget.

Reference

Look up a command

Find flags, input contracts and output fields for annotation and calibration.

Explanation

Understand the scores

Interpret reference support, competing labels, paired evidence and false-call calibration.

Explore a worked example

Examples gallery

Two runnable shell workflows with raw inputs: cohort annotation and a geometry comparison.

Notebooks gallery

Browse rendered annotation, comparison and precursor notebooks; download their source.

Use the API reference to integrate annotation into Python, consult Release notes for release changes, and read Neighbourhood score: formula and interpretation for the detailed score derivation. Native search uses seqtree; ingestion uses vdjtools.