A list of software developed for statistical and comparative analysis of mapped and clustered V(D)J rearrangements.
This is a wiki page. Please edit and add software you know about. However, note that this is not the place for closed-source commercial software vendors to advertise their products.
Command-line applications and R/Python libraries:
- Change-O (Gupta et al. 2015) - a suite for B-cell repertoire sequencing data analysis: clonal lineage and diversity analysis (Alakazam module), somatic hypermutation analysis (SHazaM module) and allele identification (TIgGER).
- VDJtools (Shugay et al. 2015) - summary statistics, repertoire diversity, clustering repertoires, CDR3 amino acid composition analysis. Mostly designed for T-cell repertoires.
- tcR (Nazarov et al. 2015) - diversity measures, shared T cell receptor sequences identification, gene usage statistics computation. R library.
- repgenHMM (Elhanati et al., 2016) - inferring repertoire generation probabilities and statistics of V(D)J rearrangement process.
GUI-base applications (immune repertoire browsers, etc):