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VDJtools

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.

Easy installation on MacOS/Linux via Homebrew or Linuxbrew:

brew tap mikessh/repseq
brew install vdjtools

List of features and detailed documentation can be found at ReadTheDocs.

Example datasets and shell scripts are provided in a separate repository.

Please cite VDJtools as:

Shugay M et al. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comp Biol 2015; 11(11):e1004503-e1004503.

VDJtools was used in the following publications:

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

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