title: VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
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.
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Shugay
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.
authors.forename: Dmitriy V
authors.initials: DV
authors.lastname: Bagaev
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Turchaninova
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.
authors.forename: Dmitriy A
authors.initials: DA
authors.lastname: Bolotin
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.|Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Britanova
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.|Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Putintseva
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.
authors.forename: Mikhail V
authors.initials: MV
authors.lastname: Pogorelyy
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|National Research University Higher School of Economics, Moscow, Russia.
authors.forename: Vadim I
authors.initials: VI
authors.lastname: Nazarov
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.|Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Zvyagin
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.
authors.forename: Vitalina I
authors.initials: VI
authors.lastname: Kirgizova
authors.affiliation: Russian Children's Hospital, Moscow, Russia.
authors.forename: Kirill I
authors.initials: KI
authors.lastname: Kirgizov
authors.affiliation: Russian Children's Hospital, Moscow, Russia.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Skorobogatova
authors.affiliation: Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.|Pirogov Russian National Research Medical University, Moscow, Russia.|Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Dmitriy M
authors.initials: DM
authors.lastname: Chudakov
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D018380:Hematopoietic Stem Cell Transplantation; D006801:Humans; D009103:Multiple Sclerosis / Q000235:genetics; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014427:Twins / Q000235:genetics; D055815:Young Adult
chemical_list: D011948:Receptors, Antigen, T-Cell