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Front Immunol. 2018 May 8;9:976. doi: 10.3389/fimmu.2018.00976. eCollection 2018.

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

Author information

1
Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States.
2
Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, United States.
3
Bank of America Corporate Center, Charlotte, NC, United States.
4
Bio5 Institute, University of Arizona, Tucson, AZ, United States.
5
Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States.
6
H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.
7
Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, United States.
8
Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
9
J. Craig Venter Institute, La Jolla, CA, United States.
10
Department of Pathology, University of California, San Diego, San Diego, CA, United States.
11
La Jolla Institute for Allergy & Immunology, La Jolla, CA, United States.

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.

KEYWORDS:

B-cell receptor; Rep-seq; T cell receptor; bioinformatics; cloud computing; immune repertoire

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