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

Content Provider	Directory of Open Access Journals (DOAJ)
Author	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
Abstract	BackgroundRecent 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.ResultsVDJServer 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.ConclusionVDJServer 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.
e-ISSN	16643224
DOI	10.3389/fimmu.2018.00976
Journal	Frontiers in Immunology
Volume Number	9
Language	English
Publisher	Frontiers Media S.A.
Publisher Date	2018-05-01
Publisher Place	Switzerland
Access Restriction	Open
Subject Keyword	Immunologic Diseases. Allergy Rep-seq Immune Repertoire Bioinformatics Cloud Computing B-cell Receptor T Cell Receptor
Content Type	Text
Resource Type	Article

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