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VDJtools: a framework for post-analysis of repertoire sequencing data

VDJtools is an open-source Java/Groovy-based framework designed to facilitate analysis of immune repertoire sequencing (RepSeq) data. VDJtools computes a wide set of statistics and is able to perform various forms of cross-sample analysis. Both comprehensive tabular output and publication-ready plots are provided.

For the period of VDJtools development, there were no other software tools able to perform a comprehensive RepSeq post-analysis. Therefore most of the analysis of this kind was done using in-house scripts, which definitely leads to "re-inventing the bicycle" problem and loss of analysis reproducibility.

The main aims of the VDJtools Project are:

  • To ensure consistency between post-analysis methods and results
  • To save the time of bioinformaticians analyzing RepSeq data
  • To create an API framework facilitating development of new RepSeq analysis applications
  • To provide a simple enough command line tool so it could be used by immunologists and biologists with little computational background

VDJtools source code and binaries are located here.

Table of Contents

.. toctree::
   :maxdepth: 2

   intro
   install
   usage
   examples
   input
   modules
   basic
   diversity
   overlap
   preprocess
   operate
   annotate
   util
   vdjviz