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Showing content from https://github.com/mikessh/vdjtools below:

mikessh/vdjtools: [Deprecated, see https://github.com/antigenomics/mirpy and other tools @antigenomics] Post-analysis of immune repertoire sequencing data

VDJtools is free for academic use. This is a legacy version, the software is no longer supported, if you need similar software solutions please visit MiLaboratory.

A comprehensive analysis framework for T-cell and B-cell repertoire sequencing data. Compiled binaries are available from here. You can download them and execute as

java -jar vdjtools.jar ...

Make sure that you've specified the full/correct path to jar file. In case of Java Heap Space exception, you can increase the JVM memory limit by adding -Xmx20G (for extra 20G) after the -jar argument.

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 ...

See homebrew-repseq for other RepSeq analysis software Homebrew installers.

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
• Plitas G et al. Regulatory T cells exhibit distinct features in human breast cancer. Immunity 2017; doi.org:10.1016/j.immuni.2016.10.032
• Izraelson M et al. Comparative Analysis of Murine T Cell Receptor Repertoires. Immunology 2017; doi.org:10.1111/imm.12857
• Bolotin DA et al. Antigen receptor repertoire profiling from RNA-seq data. Nat Biotech 2017; doi:10.1038/nbt.3979
• Meng W et al. An atlas of B-cell clonal distribution in the human body. Nat Biotech 2017; doi:10.1038/nbt.3942

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