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.

Central European Institute of Technology Masaryk University Brno Czech Republic

National Research University Higher School of Economics Moscow Russia

Pirogov Russian National Research Medical University Moscow Russia

Russian Children's Hospital Moscow Russia

Shemyakin Ovchinnikov Institute of bioorganic chemistry RAS Moscow Russia

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