VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
Mikhail Shugay(Institute of Bioorganic Chemistry), Dmitriy V. Bagaev(Institute of Bioorganic Chemistry), Maria A. Turchaninova(Pirogov Russian National Research Medical University), Dmitriy A. Bolotin(Institute of Bioorganic Chemistry), Olga V. Britanova(Institute of Bioorganic Chemistry), Ekaterina V. Putintseva(Pirogov Russian National Research Medical University), Mikhail V. Pogorelyy(Institute of Bioorganic Chemistry), Vadim I. Nazarov(Institute of Bioorganic Chemistry), Ivan V. Zvyagin(Central European Institute of Technology), Vitalina Kirgizova(Institute of Bioorganic Chemistry), К. И. Киргизов(Russian Children's Clinical Hospital), Е. В. Скоробогатова(Russian Children's Clinical Hospital), Dmitriy M. Chudakov(Central European Institute of Technology – Masaryk University)
Cited by 648Open Access
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.
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