VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements
Rounds, William H.
Toby, Inimary T.
Fonner, John M.
Levin, Mikhail K.
Mock, Stephen A.
Davila, Marco L.
Monson, Nancy L.
Scheuermann, Richard H.
Cowell, Lindsay G.
AffiliationUniv Arizona, Inst Bio5
MetadataShow full item record
PublisherFRONTIERS MEDIA SA
CitationChristley 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 and Cowell LG (2018) VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Front. Immunol. 9:976. doi: 10.3389/fimmu.2018.00976
JournalFRONTIERS IN IMMUNOLOGY
Rights© 2018 Christley, Scarborough, Salinas, Rounds, Toby, Fonner, Levin, Kim, Mock, Jordan, Ostmeyer, Buntzman, Rubelt, Davila, Monson, Scheuermann and Cowell. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at firstname.lastname@example.org.
AbstractBackground: 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.
NoteOpen access journal.
VersionFinal published version
SponsorsNIAID [AI097403, AI057229]; H. Lee Moffitt Cancer Center and Research Institute; DioGenix, Inc.; National Multiple Sclerosis Society