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VDJtools | Unifying Post-analysis of T Cell Receptor Repertoires

A complementary software suite that solves a wide range of RepSeq post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. The main aims of the VDJtools Project are: (i) Ensure consistency between post-analysis methods and results, (ii) Save the time of bioinformaticians analyzing RepSeq data, (iii) Create an API framework facilitating development of new RepSeq analysis applications, and (iv) Provide a simple enough command line tool so it could be used by immunologists and biologists with little computational background.

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VDJtools classification

  • Animals
  • Fungi
  • Plants
  • Protists

VDJtools specifications

Unique identifier:
Command line interface
Input data:
Pre-processed RepSeq data
Biological technology:
Illumina, Roche
Programming languages:
Java, R
Computer skills:
Software type:
Restrictions to use:
Output data:
RepSeq analysis results
Operating system:
Unix/Linux, Mac OS, Windows
Artistic License version 2.0

VDJtools distribution


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VDJtools support



  • Mikhail Shugay <>


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Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia

Funding source(s)

The Russian Science Foundation project №14-14-00533 (VDJtools development) and RFBR grant 13-04-00998 (cDNA libraries preparation).

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.