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

doi:10.3389/fimmu.2018.00976

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 journal › Article › peer-review

44 Scopus citations

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 language	English (US)
Article number	976
Journal	Frontiers in immunology
Volume	9
Issue number	MAY
DOIs	https://doi.org/10.3389/fimmu.2018.00976
State	Published - May 8 2018

Keywords

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

ASJC Scopus subject areas

Immunology and Allergy
Immunology

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10.3389/fimmu.2018.00976

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Christley, S., Scarborough, W., Salinas, E., Rounds, W. H., Toby, I. T., Fonner, J. M., Levin, M. K., Kim, M., Mock, S. A., Jordan, C., Ostmeyer, J., Buntzman, A., Rubelt, F., Davila, M. L., Monson, N. L., Scheuermann, R. H., & Cowell, L. G. (2018). VDJServer: A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements. Frontiers in immunology, 9(MAY), Article 976. https://doi.org/10.3389/fimmu.2018.00976

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

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

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, Bioinformatics, Cloud computing, Immune repertoire, Rep-seq, T cell receptor",

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

note = "Publisher Copyright: {\textcopyright} 2018 Christley, Scarborough, Salinas, Rounds, Toby, Fonner, Levin, Kim, Mock, Jordan, Ostmeyer, Buntzman, Rubelt, Davila, Monson, Scheuermann and Cowell.",

year = "2018",

month = may,

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doi = "10.3389/fimmu.2018.00976",

language = "English (US)",

volume = "9",

journal = "Frontiers in immunology",

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T2 - A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements

AU - Christley, Scott

AU - Scarborough, Walter

AU - Salinas, Eddie

AU - Rounds, William H.

AU - Toby, Inimary T.

AU - Fonner, John M.

AU - Levin, Mikhail K.

AU - Kim, Min

AU - Mock, Stephen A.

AU - Jordan, Christopher

AU - Ostmeyer, Jared

AU - Buntzman, Adam

AU - Rubelt, Florian

AU - Davila, Marco L.

AU - Monson, Nancy L.

AU - Scheuermann, Richard H.

AU - Cowell, Lindsay G.

PY - 2018/5/8

Y1 - 2018/5/8

N2 - 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.

AB - 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.

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KW - Bioinformatics

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KW - Immune repertoire

KW - Rep-seq

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

Abstract

Keywords

ASJC Scopus subject areas

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