A comprehensive analysis framework for T-cell and B-cell repertoire sequencing data. Compiled binaries are available from here. The software is cross-platform and requires Java v1.8 to run and R to perform plotting.
Easy installation on MacOS/Linux via Homebrew or Linuxbrew:
brew tap homebrew/science
brew tap mikessh/repseq
brew install vdjtools
vdjtools CalcBasicStats ...For Windows just use the latest VDJtools bundle marked with .win.zip suffix.
List of features and detailed documentation can be found at ReadTheDocs.
Example datasets and shell scripts are provided in a separate repository.
Shugay M et al. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comp Biol 2015; 11(11):e1004503-e1004503.
- Feng Y et al. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature 2015; doi:10.1038/nature16141
- Britanova OV et al. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J Immunol 2016; doi:10.4049/jimmunol.1600005
- Joachims ML et al. Single-cell analysis of glandular T cell receptors in Sjögren’s syndrome. JCI Insight 2016; doi:10.1172/jci.insight.85609