Antigen Receptor Galaxy (ARGalaxy)

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Scope:
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.

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