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VDJviz: a versatile browser for immunogenomics data.

Dmitriy V Bagaev1, Ivan V Zvyagin1,2,3, Ekaterina V Putintseva1,3

  • 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.

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Summary
This summary is machine-generated.

VDJviz is a new web tool for analyzing immune repertoire sequencing (Rep-Seq) data. It simplifies the exploration of T- and B-cell receptor diversity and aids in quality control for immunological research.

Keywords:
B-cellBrowserHigh-throughput sequencingImmunologyRepertoire sequencingT-cell

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Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • Adaptive immunity relies on T- and B-cell receptor sequences for antigen specificity.
  • High-throughput immune repertoire sequencing (Rep-Seq) profiles millions of antigen receptors.
  • Existing Rep-Seq analysis tools often lack user-friendliness for researchers without extensive computational backgrounds.

Purpose of the Study:

  • To introduce VDJviz, an intuitive web tool for analyzing and quality controlling Rep-Seq data.
  • To provide researchers with a flexible platform for in-depth immune repertoire profiling.
  • To facilitate the exploration of key repertoire characteristics and detection of data biases.

Main Methods:

  • Development of a web-based tool, VDJviz.
  • Utilizing real-world Rep-Seq data for demonstration and validation.
  • Implementation of features for analyzing spectratype, clonality, V-(D)-J recombination, and shared clonotypes.

Main Results:

  • VDJviz enables browsing, analysis, and quality control of Rep-Seq results from various pre-processing pipelines.
  • The tool facilitates exploration of repertoire characteristics like spectratype and clonality.
  • VDJviz effectively identifies shared clonotypes and detects biases such as artificial diversity and cross-sample contamination.

Conclusions:

  • VDJviz is a versatile and lightweight tool for routine analysis and quality control of Rep-Seq data.
  • It is suitable for biologists, immunologists, and immunogeneticists.
  • The software is freely available for non-commercial use.