| ARGalaxy is a collection of tools for analyses and visualization of T- and B-cell receptor repertoire sequencing data of 13 different species. It consists of four parts that can be run combined or independently, depending on the available data and the research question. The demultiplex tool allows data trimming and demultiplexing whilst with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published IGGalaxy virtual machine which was developed to visualize V(D)J gene usage. It requires fasta files, IMGT/HighV-QUEST output files, or output files from the SHM&CSR pipeline and allows analysis of both B-cell and T-cell receptor rearrangements and visualises CDR3 characteristics (length and amino acid usage), junction characteristics and calculates the diversity of the immune repertoire. Finally, the ARGalaxy includes the newly developed SHM&CSR pipeline to analyze 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 based on IMGT/HighV-QUEST .txz files as input.
These tools are available for use on our own server: https://argalaxy.researchlumc.nl To use the lymphclone package to determine clonality, the "imperial-college-research-computing" channel should be added to the allowed channels for Galaxy. |
hg clone https://toolshed.g2.bx.psu.edu/repos/davidvanzessen/argalaxy_tools
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| 1.1.4 | 16.04 | ||