Features and workflow




As the core framework is complied into Java™ bytecode, it could in theory be run on any platform that has a Java Runtime Environment installed. The software is distributed in a form of an executable JAR file.

Note that the graphical output requires R programming language and corresponding modules to be installed.

See the Installing VDJtools section for more details.


VDJtools could be run on most of commodity hardware setups and is optimized to take advantage of parallel computations. The pipeline was successfully stress-tested using ~70 diverse samples containing repertoire snapshot of around 500,000 human T-cells on a UNIX server with 2x Intel Xeon E5-1620 and 64 Gb RAM.


The framework is currently able to import and analyze the output of the following V-(D)-J junction mapping software and analysis platforms:

  • MiTCR
  • MiGEC
  • IgBlast (via our MIGMAP wrapper)
  • IMGT
  • ImmunoSEQ
  • VDJdb
  • Vidjil
  • RTCR
  • MiXCR
  • ImSEQ

For more details see the software section. VDJtools converts those files to its internal format (see VDJtools format) which is used throughout the pipeline.


If this list is missing your favourite RepSeq processing software, please add a corresponding feature request Any contributions in form of pull requests are also welcome.