VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

PLoS Comput Biol. 2015 Nov 25;11(11):e1004503. doi: 10.1371/journal.pcbi.1004503. eCollection 2015 Nov.

Abstract

Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

MeSH terms

  • Adolescent
  • Adult
  • Child
  • Cluster Analysis
  • Computational Biology / methods*
  • Hematopoietic Stem Cell Transplantation
  • Humans
  • Multiple Sclerosis / genetics
  • Receptors, Antigen, T-Cell / chemistry*
  • Receptors, Antigen, T-Cell / genetics*
  • Receptors, Antigen, T-Cell / metabolism
  • Sequence Analysis, DNA / methods*
  • Software*
  • Twins / genetics
  • Young Adult

Substances

  • Receptors, Antigen, T-Cell

Grant support

This work was supported by the Russian Science Foundation project №14-14-00533 (VDJtools development) and RFBR grant 13-04-00998 (cDNA libraries preparation). The work was carried out in part using equipment provided by the Shemyakin– Ovchinnikov Institute of Bioorganic Chemistry Core Facility. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.