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2016 ; 17
(ä): 453
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VDJviz: a versatile browser for immunogenomics data
#MMPMID27297497
Bagaev DV
; Zvyagin IV
; Putintseva EV
; Izraelson M
; Britanova OV
; Chudakov DM
; Shugay M
BMC Genomics
2016[Jun]; 17
(ä): 453
PMID27297497
show ga
BACKGROUND: The 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.
RESULTS: Here 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.
CONCLUSIONS: VDJviz 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 .
free
free
free
