Tools and Resources

Here are links to some of the tools and resources I’ve made for various tasks in TCR research.

Tool / Resource	Purpose
`stitchr`	Generate full-length coding TCR sequences from V/J/CDR3 classifiers, for functional validation or high-throughput modelling.
`autoDCR`	Flexible V/J/CDR3 annotation from deep sequencing data. A custom fork of the Chain lab’s Decombinator tool, that matches tags along the entire length of TCR variable domains, allowing full allele-level determination, and other more niche applications (e.g. novel allele/splice detection).
`immunoseq2airr`	Convert Adaptive Biotech’s immunoSEQ format TCR data to the Adaptive Immune Receptor Repertoire-Community (AIRR-C) standard format.
`IMGTgeneDL`	Automated downloading of TCR/IG sequences from `IMGT/GENE-DB`.
`genedb-releases`	Banked snapshots of the entirety of `IMGT/GENE-DB` (i.e. both TCR and IG, all species/loci), to allow comparison between versions and reproduction of historical analyses.
`novel-tcr-alleles`	Collated resource of published novel TCR alleles.
`airrc2hlaguessr`	Convert AIRR-C format data into that required for `HLAGuessr`.
`vdjrearranger`	Generate synthetic 10X V(D)J FASTQ data, for generating standards with which to test different germline reference sets.

Alternatively all of my repositories and contributions can be seen via my Github page.