VDJtools is an excellent tool for comprehensive comparative post analysis of T-cell receptor repetoires.
The software computes a wide set of statistics and is able to perform various forms of cross-sample analysis. Both comprehensive tabular output and presentation/publication-ready plots are provided.
Before VDJtools most of the analysis of this kind was done using in-house scripts, which inevitably led to reinventing the wheel and loss of analysis reproducibility.
The aims of VDJtools are:
- to ensure consistency between post-analysis methods and results
- to save time of bioinformaticians analyzing TCR repertoire data
- to provide a simple enough command line tool so it could be used by immunologists and biologists with little computational background
VDJtools accepts tabular output of commonly used pre-processing software: MIGEC, MiXCR, MiTCR, ImmunoSEQ, and IMGT/HighV-QUEST.
Please see documentation for details.
Cite VDJtools as:
Shugay M et al. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comp Biol 2015; 11(11) doi: 10.1371/journal.pcbi.1004503.
For commercial use please contact licensing@milaboratory.com.
Image from Shugay et al., 2015, PLoS Comp Biol, doi: 10.1371/journal.pcbi.1004503.