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Post-analysis of immune repertoire sequencing data
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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.

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.

Some recent publications where VDJtools was used:

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