Antigen Receptor Galaxy (ARGalaxy)
Launch Galaxy
| Public Server: | Antigen Receptor Galaxy (ARGalaxy) (NL) |
|---|---|
| Scope: | Tool Publishing |
| Summary: | Automate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data. |
Comments
- Consists of four parts: the demultiplex tool, the IMGT concatenate tool, the immune repertoire pipeline and the SHM&CSR pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, dependent on the available data and the question of interest
- The demultiplex tool allows data trimming and demultiplexing of samples
- The concatenate tool allows the merging of multiple IMGT/HighV-QUEST output files into a single file.
- The immune repertoire pipeline allows analysis of both B- and T-cell receptor rearrangements and was developed to visualize V(D)J gene usage, CDR3 characteristics (length and amino acid usage), junction characteristics and calculate the diversity of the immune repertoire.
- The SHM&CSR pipeline allows analysis of somatic hypermutations (SHM) and/or class switch recombination (CSR) in B-cell receptor rearrangements. It analyzes the frequency and patterns of SHM, antigen selection (including BASELINe), clonality (Change-O) and CSR.
User Support
- Contact David van Zessen
Quotas
- Account creation required. Anyone can create an account.
Citations
- Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data, Hanna IJspeert, Pauline A. van Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Andrew P. Stubbs and Mirjam van der Burg J Immunol May 15, 2017, 198 (10) 4156-4165; DOI:10.4049/jimmunol.1601921
- ARGalaxy tagged publications in the Galaxy Publication Library
Sponsors
- Departments of Immunology and Bioinformatics at Erasmus MC.