T Cell receptor sequencing

Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM.
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
PLoS Comput Biol. 2015 Nov 25;11(11):e1004503.

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.

The T cell receptor is composed of an alpha chain and a beta chain and these are made from joining constant joing (J), Diversity (D) and variable (V) region genes. These can be sequenced and at some stage we will be able to work out what they are responding to in the future