A comprehensive framework for post-analysis of immune 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.
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; epub before print doi:10.1038/nature16141