title: TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization.
abstract: The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. To decipher the complexity of TCR repertoire, we developed an integrated pipeline, TCRklass, using K-string-based algorithm that has significantly improved the accuracy and performance over existing tools. We tested TCRklass using manually curated short read datasets in comparison with in silico datasets; it showed higher precision and recall rates on CDR3 identification. We applied TCRklass on large datasets of two human and three mouse TCR repertoires; it demonstrated higher reliability on CDR3 identification and much less biased V/J profiling, which are the two components contributing the diversity of the repertoire. Because of the sequencing cost, short paired-end reads generated by next-generation sequencing technology are and will remain the main source of data, and we believe that the TCRklass is a useful and reliable toolkit for TCR repertoire analysis.
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China;
authors.forename: Xi
authors.initials: X
authors.lastname: Yang
authors.affiliation: Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Di
authors.initials: D
authors.lastname: Liu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Na
authors.initials: N
authors.lastname: Lv
authors.affiliation: Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Jing
authors.initials: J
authors.lastname: Zou
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Xue
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Peipei
authors.initials: P
authors.lastname: Liu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Jing
authors.initials: J
authors.lastname: Gao
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; and.
authors.forename: Yongfei
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Yi
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
authors.forename: Ruifen
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.affiliation: Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; zhubaoli@im.ac.cn gaof@im.ac.cn ma@im.ac.cn.
authors.forename: Juncai
authors.initials: J
authors.lastname: Ma
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; and Chinese Center for Disease Control and Prevention, Beijing 102206, China zhubaoli@im.ac.cn gaof@im.ac.cn ma@im.ac.cn.
authors.forename: George F
authors.initials: GF
authors.lastname: Gao
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; and zhubaoli@im.ac.cn gaof@im.ac.cn ma@im.ac.cn.
authors.forename: Baoli
authors.initials: B
authors.lastname: Zhu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001330:Electronic Data Processing / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D011948:Receptors, Antigen, T-Cell / Q000032:analysis / Q000235:genetics* / Q000276:immunology; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D060152:V(D)J Recombination / Q000235:genetics*
chemical_list: D011948:Receptors, Antigen, T-Cell