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1 # ARGalaxy Immune Repertoire
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2 This is the GitHub repository for the ARGalaxy Immune repertoire pipeline.
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3 The Galaxy tool version can be found [here](https://toolshed.g2.bx.psu.edu/repository/browse_repositories_i_own?sort=name&operation=view_or_manage_repository&id=2e457d63170a4b1c).
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4 The docker version can be found [here](https://github.com/ErasmusMC-Bioinformatics/ARGalaxy-docker).
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5
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6 ## Overview
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7
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8 In execution order:
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9
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10 #### imgt_loader or igblast
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11
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12 ###### imgt_loader (Recommended)
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13 Start the analysis with [IMGT HighV Quest](https://www.imgt.org/HighV-QUEST/) archives.
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14 An IMGT archive file holds [multiple tabular files](http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#output3), this script extracts the specific columns relevant to the analysis from several of these files.
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15
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16 `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`
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17
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18
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19 ###### igblast
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20 Start the analysis with FASTA files that are aligned with [igblast](https://www.ncbi.nlm.nih.gov/igblast/).
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21 Note that this method will provide less information than the IMGT archive.
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22
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23 `sh igblast.sh /path/to/sequences.fasta species locus /path/to/output.txt`
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24
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25 #### experimental_design
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26 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.
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27
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28 `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`
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29
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30 #### report_clonality
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31 The R script that creates the analysis result.
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32
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33 `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"`
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34
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35 ###### parameters
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36 Clonaltype:
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37 - none
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38 - Top.V.Gene,CDR3.Seq
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39 - Top.V.Gene,CDR3.Seq.DNA
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40 - Top.V.Gene,Top.J.Gene,CDR3.Seq
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41 - Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA
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42 - Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA
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43
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44 Species:
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45 - Homo sapiens functional
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46 - Homo sapiens
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47 - Homo sapiens non-functional
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48 - Bos taurus
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49 - Bos taurus functional
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50 - Bos taurus non-functional
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51 - Camelus dromedarius
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52 - Camelus dromedarius functional
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53 - Camelus dromedarius non-functional
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54 - Canis lupus familiaris
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55 - Canis lupus familiaris functional
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56 - Canis lupus familiaris non-functional
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57 - Danio rerio
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58 - Danio rerio functional
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59 - Danio rerio non-functional
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60 - Macaca mulatta
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61 - Macaca mulatta functional
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62 - Macaca mulatta non-functional
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63 - Mus musculus
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64 - Mus musculus functional
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65 - Mus musculus non-functional
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66 - Mus spretus
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67 - Mus spretus functional
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68 - Mus spretus non-functional
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69 - Oncorhynchus mykiss
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70 - Oncorhynchus mykiss functional
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71 - Oncorhynchus mykiss non-functional
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72 - Ornithorhynchus anatinus
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73 - Ornithorhynchus anatinus functional
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74 - Ornithorhynchus anatinus non-functional
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75 - Oryctolagus cuniculus
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76 - Oryctolagus cuniculus functional
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77 - Oryctolagus cuniculus non-functional
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78 - Rattus norvegicus
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79 - Rattus norvegicus functional
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80 - Rattus norvegicus non-functional
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81 - Sus scrofa
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82 - Sus scrofa functional
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83 - Sus scrofa non-functional
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84
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85 Locus:
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86 - TRA
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87 - TRD
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88 - TRG
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89 - TRB
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90 - IGH
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91 - IGI
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92 - IGK
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93 - IGL
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94
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95 Filter productive:
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96 - yes
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97 - no
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98
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99 Clonality Method:
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100 - none
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101 - old
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102 - boyd
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103
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104 ## complete.sh
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105 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.
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106
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107 `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`
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108 See "report_clonality" for the parameter options.
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109
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110 ## Dependencies
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111 - Linux
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112 - R
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113 - gridExtra
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114 - ggplot2
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115 - plyr
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116 - data.table
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117 - reshape2
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118 - lymphclon
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119
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120 #### optional
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121 - Circos
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122 - IgBlast
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123 - igblastwrp
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