VDJviz: a versatile browser for immunogenomics data

BMC Genomics

Software

Dmitriy V. Bagaev¹  Ekaterina V. Putintseva²  Mikhail Shugay³  Mark Izraelson⁴  Olga V. Britanova⁴  Ivan V. Zvyagin⁴  Dmitriy M. Chudakov⁴ 

[1] Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997, Moscow, Russia;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997, Moscow, Russia;Central European Institute of Technology, Masaryk University, Brno, Czech republic;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997, Moscow, Russia;Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997, Moscow, Russia;Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia;Central European Institute of Technology, Masaryk University, Brno, Czech republic;

关键词: High-throughput sequencing;    Immunology;    Browser;    T-cell;    B-cell;    Repertoire sequencing;   

DOI  :  10.1186/s12864-016-2799-7

 received in 2015-12-01, accepted in 2016-05-25,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile millions of antigen receptors of an individual in a single experiment. While a substantial number of tools for mapping and assembling Rep-Seq data were published recently, the field still lacks an intuitive and flexible tool that can be used by researchers with little or no computational background for in-depth analysis of immune repertoire profiles.ResultsHere we report VDJviz, a web tool that can be used to browse, analyze and perform quality control of Rep-Seq results generated by various pre-processing software. On a set of real data examples we show that VDJviz can be used to explore key repertoire characteristics such as spectratype, repertoire clonality, V-(D)-J recombination patterns and to identify shared clonotypes. We also demonstrate the utility of VDJviz in detection of critical Rep-Seq biases such as artificial repertoire diversity and cross-sample contamination.ConclusionsVDJviz is a versatile and lightweight tool that can be easily employed by biologists, immunologists and immunogeneticists for routine analysis and quality control of Rep-Seq data. The software is freely available for non-commercial purposes, and can be downloaded from: https://github.com/antigenomics/vdjviz.

【 授权许可】

CC BY   
© The Author(s). 2016