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ARGalaxy specifications

Information


Unique identifier OMICS_33265
Name ARGalaxy
Alternative name Antigen Receptor Galaxy
Interface Web user interface
Restrictions to use None
Programming languages Python, R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Mirjam van der Burg
  • person_outline David van Zessen

Publication for Antigen Receptor Galaxy

ARGalaxy citations

 (4)
library_books

Immunodeficiency in Bloom’s Syndrome

2017
PMCID: 5742600
PMID: 29098565
DOI: 10.1007/s10875-017-0454-y

[…] according the manufacturer’s recommendations. Sequences were demultiplexed based on their multiplex identifier sequence and 40 nucleotides trimmed from both sides to remove the primer sequence using ARGalaxy [] (https://bioinf-galaxian.erasmusmc.nl/argalaxy). Fasta files were uploaded in IMGT/High-V-Quest [], and subsequently the IMGT output files were analyzed in ARGalaxy []. Only productive seq […]

library_books

VDJPipe: a pipelined tool for pre processing immune repertoire sequencing data

2017
BMC Bioinformatics
PMCID: 5637252
PMID: 29020925
DOI: 10.1186/s12859-017-1853-z

[…] o V, D, and J assignment, 2) those specializing in specific pre-processing operations, and 3) those providing generic pre-processing operations. We excluded web analysis portals such as VDJServer and ARGalaxy, as they provide web-based access to other tools. We indicate each tool’s category (1, 2 or 3) in Table . All of the tools in the first category provide some limited pre-processing capability […]

library_books

Human IgG2 and IgG4 expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age

2017
Immunol Cell Biol
PMCID: 5636940
PMID: 28546550
DOI: 10.1038/icb.2017.43

[…] s recommendations.Data analysis was performed as previously described by IJspeert et al 2016. In short, sequences were demultiplexed based on their multiplex identifier sequence and trimmed using the Antigen Receptor Galaxy (ARGalaxy) tool. Fasta files were uploaded in IMGT/High V-Quest, and subsequently, the IMGT output files were analyzed in the IGGalaxy tool. To exclude low-quality reads, we on […]

library_books

Evaluation of the Antigen Experienced B Cell Receptor Repertoire in Healthy Children and Adults

2016
Front Immunol
PMCID: 5066086
PMID: 27799928
DOI: 10.3389/fimmu.2016.00410

[…] leles, search for insertions and deletions: yes, parameters for IMGT/Junction Analysis: default) (), and subsequently, the IMGT output files were analyzed in an extended version of our IGGalaxy tool (ARGalaxy) (). Information on junction characteristics, CDR3 length and composition, CSR, the number of mutations, and SHM patterns were obtained. Only productive sequences, that were complete, without […]

Citations

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ARGalaxy institution(s)
Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, the Netherlands
ARGalaxy funding source(s)
Supported by Dutch Organization for Scientific Research Vidi Grant 91712323 and Veni Grant 91616058.

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