VDJServer: A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements

Scott Christley, Walter Scarborough, Eddie Salinas, William H. Rounds, Inimary T. Toby, John M. Fonner, Mikhail K. Levin, Min Kim, Stephen A. Mock, Christopher Jordan, Jared Ostmeyer, Adam Buntzman, Florian Rubelt, Marco L. Davila, Nancy L. Monson, Richard H. Scheuermann, Lindsay G. Cowell

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. Results: VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. Conclusion: VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.

Original languageEnglish (US)
Article number976
JournalFrontiers in Immunology
Volume9
Issue numberMAY
DOIs
StatePublished - May 8 2018

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Workflow
Information Dissemination
Software
Computing Methodologies
Web Browser
Adaptive Immunity
Allergy and Immunology
Computational Biology
Autoimmunity
Quality Control
B-Lymphocytes
Research Personnel
T-Lymphocytes
Health
Genes
Neoplasms
Datasets

Keywords

  • B-cell receptor
  • Bioinformatics
  • Cloud computing
  • Immune repertoire
  • Rep-seq
  • T cell receptor

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

Cite this

VDJServer : A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements. / Christley, Scott; Scarborough, Walter; Salinas, Eddie; Rounds, William H.; Toby, Inimary T.; Fonner, John M.; Levin, Mikhail K.; Kim, Min; Mock, Stephen A.; Jordan, Christopher; Ostmeyer, Jared; Buntzman, Adam; Rubelt, Florian; Davila, Marco L.; Monson, Nancy L.; Scheuermann, Richard H.; Cowell, Lindsay G.

In: Frontiers in Immunology, Vol. 9, No. MAY, 976, 08.05.2018.

Research output: Contribution to journalArticle

Christley, S, Scarborough, W, Salinas, E, Rounds, WH, Toby, IT, Fonner, JM, Levin, MK, Kim, M, Mock, SA, Jordan, C, Ostmeyer, J, Buntzman, A, Rubelt, F, Davila, ML, Monson, NL, Scheuermann, RH & Cowell, LG 2018, 'VDJServer: A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements', Frontiers in Immunology, vol. 9, no. MAY, 976. https://doi.org/10.3389/fimmu.2018.00976
Christley, Scott ; Scarborough, Walter ; Salinas, Eddie ; Rounds, William H. ; Toby, Inimary T. ; Fonner, John M. ; Levin, Mikhail K. ; Kim, Min ; Mock, Stephen A. ; Jordan, Christopher ; Ostmeyer, Jared ; Buntzman, Adam ; Rubelt, Florian ; Davila, Marco L. ; Monson, Nancy L. ; Scheuermann, Richard H. ; Cowell, Lindsay G. / VDJServer : A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements. In: Frontiers in Immunology. 2018 ; Vol. 9, No. MAY.
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