Vdjtools

This software is deprecated

This software is no longer actively developed and maintained. For immune repertoire sequencing (AIRR-seq) data analysis software alternatives see other tools by Immunosequencing Algorithms laboratory:

• mirpy a library with useful python modules and functions for analysis of AIRR-seq data
• vdjmatch2 for fast querying and matching clonotypes across large AIRR-seq datasets and annotating repertoires using VDJdb database
• vdjtools2 re-implementing all VDJtools analysis methods and more! - coming soon
• redcea and irrm-codec implementing smart adaptive immune receptor sequence embeddings and extended TCRNET algorithm coming soon

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VDJtools

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:

• 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