ARGalaxy Immune Repertoire

This is the GitHub repository for the ARGalaxy Immune repertoire pipeline.
The Galaxy tool version can be found here.
The docker version can be found here.

Overview

In execution order:

imgt_loader or igblast

imgt_loader (Recommended)

Start the analysis with IMGT HighV Quest archives.
An IMGT archive file holds multiple tabular files, this script extracts the specific columns relevant to the analysis from several of these files.

Rscript imgt_loader.r 1_Summary.txt 3_Nt-sequences.txt 5_AA-sequences.txt 6_Junction.txt 4_IMGT-gapped-AA-sequences.txt /path/to/output.txt

igblast

Start the analysis with FASTA files that are aligned with igblast.
Note that this method will provide less information than the IMGT archive.

sh igblast.sh /path/to/sequences.fasta species locus /path/to/output.txt

experimental_design

This script will merge multiple result files (from the last step) into a single file with an additional ID and Replicate column to differentiate the individual samples during the analysis and to allow for analysis across samples.

Rscript experimental_design.r /path/to/input_1 id_1 [/path/to/input_2 id_2] [/path/to/input_n id_n] /path/to/output

report_clonality

The R script that creates the analysis result.

sh r_wrapper.sh /path/to/experimental_design/output.txt /path/to/output_dir/output.html /path/to/output_dir "clonaltype" "species" "locus" "filter_productive" "clonality_method"

parameters

Clonaltype:

• none
• Top.V.Gene,CDR3.Seq
• Top.V.Gene,CDR3.Seq.DNA
• Top.V.Gene,Top.J.Gene,CDR3.Seq
• Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA
• Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA

Species:

• Homo sapiens functional
• Homo sapiens
• Homo sapiens non-functional
• Bos taurus
• Bos taurus functional
• Bos taurus non-functional
• Camelus dromedarius
• Camelus dromedarius functional
• Camelus dromedarius non-functional
• Canis lupus familiaris
• Canis lupus familiaris functional
• Canis lupus familiaris non-functional
• Danio rerio
• Danio rerio functional
• Danio rerio non-functional
• Macaca mulatta
• Macaca mulatta functional
• Macaca mulatta non-functional
• Mus musculus
• Mus musculus functional
• Mus musculus non-functional
• Mus spretus
• Mus spretus functional
• Mus spretus non-functional
• Oncorhynchus mykiss
• Oncorhynchus mykiss functional
• Oncorhynchus mykiss non-functional
• Ornithorhynchus anatinus
• Ornithorhynchus anatinus functional
• Ornithorhynchus anatinus non-functional
• Oryctolagus cuniculus
• Oryctolagus cuniculus functional
• Oryctolagus cuniculus non-functional
• Rattus norvegicus
• Rattus norvegicus functional
• Rattus norvegicus non-functional
• Sus scrofa
• Sus scrofa functional
• Sus scrofa non-functional

Locus:

• TRA
• TRD
• TRG
• TRB
• IGH
• IGI
• IGK
• IGL

Filter productive:

• yes
• no

Clonality Method:

• none
• old
• boyd

complete.sh

This script will run all of the above for you, it will detect if you are using FASTA files or IMGT archives and use the appropriate tools.

sh complete.sh /path/to/input_1 id_1 [/path/to/input_n id_n] /path/to/out_dir/out.html /path/to/out_dir clonaltype species locus filter_productive clonality_method
See "report_clonality" for the parameter options.

Dependencies

• Linux
• R
  • gridExtra
  • ggplot2
  • plyr
  • data.table
  • reshape2
  • lymphclon

optional

• Circos
• IgBlast
• igblastwrp