VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. - Mikhail Shugay; Dmitriy V. Bagaev; Maria A. Turchaninova; Dmitriy A. Bolotin; Olga V. Britanova; Ekaterina V. Putintseva; Mikhail V. Pogorelyy; Vadim I. Nazarov; Ivan V. Zvyagin; Vitalina I. Kirgizova; Kirill I. Kirgizov; Elena V. Skorobogatova; et al. (PLoS Comput. Biol., 2015)

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. - Mikhail Shugay; Andrew R. Zaretsky; Dmitriy A. Shagin; Irina A. Shagina; Ivan A. Volchenkov; Andrew A. Shelenkov; Mikhail Y. Lebedin; Dmitriy V. Bagaev; Sergey A. Lukyanov; Dmitry M. Chudakov (PLoS Comput. Biol., 2017)

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. - Mikhail Shugay; Dmitriy V. Bagaev; Ivan V. Zvyagin; Renske M. A. Vroomans; Jeremy Chase Crawford; Garry Dolton; Ekaterina Komech; Anastasiya L. Sycheva; Anna E. Koneva; Evgeniy S. Egorov; Alexey V. Eliseev; Ewald van Dyk; et al. (Nucleic Acids Res., 2018)