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Introduction

Features and workflow

_static/images/framework.png

Prerequisites

Software

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 :ref:`install` section for more details.

Hardware

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.

Input

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 :ref:`software` section. VDJtools converts those files to its internal format (see :ref:`vdjtools_format`) which is used throughout the pipeline.

Note

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.

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