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¶
- Installing VDJtools
- Analysis modules
- Basic analysis
- Diversity estimation
- Repertoire overlap analysis
- Operate on clonotype tables
- Clonotype browser