VDJtools: Unifying post-analysis of T cell receptor repertoires

• Authors: SHUGAY Mikhail; BAGAEV Dimitriy V.; TURCHANINOVA Maria A.; BOLOTIN Dmitry; BRITANOVA Olga; PUTINTSEVA Ekaterina V.; POGORELYY Mikhail V.; NAZAROV Vadim I.; ZVYAGIN Ivan V.; KIRGIZOVA Vitalina I.; KIRGIZOV Kirill I.; SKOROBOGATOVA Elena V.; CHUDAKOV Dmitriy
• Year of publication: 2015
• Type: Article in Periodical
• Magazine / Source: PLOS Computational Biology
• MU Faculty or unit: Central European Institute of Technology
• Web: http://www.ploscompbiol.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pcbi.1004503&representation=PDF
• Doi: http://dx.doi.org/10.1371/journal.pcbi.1004503
• Field: Biochemistry
• Keywords: VDJtools; T cell; receptor repertoires; TCR
• Description: 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.