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 :ref:`install` 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:
- IgBlast (via our MIGMAP wrapper)
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.