Post-analysis of immune repertoire sequencing data
VDJtools is free for academic use. his 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.