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1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8.2" >
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2 <stdio>
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3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
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4 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
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5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
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6 <exit_code range="1:" level="fatal" description="Error" />
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7 </stdio>
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8 <description>Identification of genomic tandem repeats from NGS data</description>
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9 <requirements>
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10 <requirement type="package">imagemagick</requirement>
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11 <requirement type="package">mafft</requirement>
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12 <requirement type="package">blast</requirement>
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13 <requirement type="package" version="0.9.29">diamond</requirement>
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14 <requirement type="package">blast-legacy</requirement>
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15 <requirement type="package">r-igraph</requirement>
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16 <requirement type="package">r-data.tree</requirement>
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17 <requirement type="package">r-stringr</requirement>
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18 <requirement type="package">r-r2html</requirement>
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19 <requirement type="package">r-hwriter</requirement>
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20 <requirement type="package">r-dt</requirement>
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21 <requirement type="package">r-scales</requirement>
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22 <requirement type="package">r-plotrix</requirement>
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23 <requirement type="package">r-png</requirement>
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24 <requirement type="package">r-plyr</requirement>
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25 <requirement type="package">r-dplyr</requirement>
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26 <requirement type="package">r-optparse</requirement>
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27 <requirement type="package">r-dbi</requirement>
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28 <requirement type="package">r-rsqlite</requirement>
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29 <requirement type="package">r-rserve</requirement>
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30 <requirement type="package">bioconductor-biostrings</requirement>
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31 <requirement type="package" version="2.3.8.1">repex_tarean</requirement>
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32 <requirement type="set_environment">REPEX</requirement>
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33 <requirement type="set_environment">REPEX_VERSION</requirement>
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34 <requirement type="package" version="0.9.1">pyrserve</requirement>
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35 </requirements>
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36 <command detect_errors="exit_code">
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37 export PYTHONHASHSEED=0;
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38 \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
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39 #if $advanced_options.advanced:
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40 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
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41 #if $advanced_options.custom_library.options_custom_library :
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42 -d $advanced_options.custom_library.library extra_database
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43 #end if
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44 #if $advanced_options.options.options:
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45 -opt $advanced_options.options.options
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46 #end if
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47 #else:
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48 -M 0.2
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49
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50 #end if
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51 ${FastaFile} >stdout.log 2> stderr.log ;
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52 echo "STDOUT CONTENT:" >> ${log} ;
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53 cat stdout.log >> ${log} ;
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54 echo "STDERR CONTENT:" >> ${log} ;
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55 cat stderr.log >> ${log} &&
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56 \${REPEX}/stderr_filter.py stderr.log &&
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57 cd tarean_output &&
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58 zip -fz -r ${ReportArchive}.zip * &&
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59 mv ${ReportArchive}.zip ${ReportArchive} &&
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60 cp index.html ${ReportFile} &&
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61 mkdir ${ReportFile.files_path} &&
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62 cp -r --parents libdir ${ReportFile.files_path} &&
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63 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &&
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64 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &&
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65 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &&
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66 cp *.png ${ReportFile.files_path}/ &&
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67 cp *.csv ${ReportFile.files_path}/ &&
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68 cp *.html ${ReportFile.files_path}/ &&
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69 cp *.css ${ReportFile.files_path}/ &&
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70 cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || :
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71
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72
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73 </command>
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74
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75 <inputs>
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76 <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta"
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77 help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/>
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3
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78
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4
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79 <conditional name="read_sampling">
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80 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
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81 <when value="false">
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3
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82 <!-- pass -->
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83 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
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3
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84 </when>
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85 <when value="true">
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86 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
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87 </when>
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88 </conditional>
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89
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90 <conditional name="advanced_options">
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91 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
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92 <when value="false">
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93 <!-- pass -->
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94 </when>
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95 <when value="true">
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96 <param name="merging" type="boolean" truevalue="0.2" falsevalue="0" checked="True" label="Perform cluster merging" help="By default, clusters connected through paired-end reads are merged"/>
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97 <conditional name="custom_library">
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98 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
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99 <when value="false">
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100 <!-- do nothing here -->
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101 </when>
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102 <when value="true">
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103 <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/>
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104 </when>
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105 </conditional>
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106 <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/>
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107 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
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108 <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option if you want to keep original names."/>
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109 <conditional name="options">
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110 <param name="options" type="select" label="Similarity search options">
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111 <option value="ILLUMINA" selected="true">Default </option>
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112 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
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113
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114 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> -->
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115 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> -->
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116 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
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117 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
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118 <!-- </option> -->
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119 </param>
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120 </conditional>
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121 </when>
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122 </conditional>
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123
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124 <conditional name="queue_definition">
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125 <param name="queue_select" type="select" label="Select queue">
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126 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
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127 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
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128 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
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129 </param>
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130 <when value="basic_fast_queue">
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131 <param name="queue_specification" type="text" label="Modify parameters (optional)"
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132 value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" />
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133 </when>
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134
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135 <when value="long_slow_queue">
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136 <param name="queue_specification" type="text" label="Modify parameters (optional)"
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137 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
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138 </when>
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139 <when value="extra_long_slow_queue">
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140 <param name="queue_specification" type="text" label="Modify parameters (optional)"
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141 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
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142 </when>
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143 </conditional>
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144
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145
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146
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147 </inputs>
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148 <outputs>
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149 <data name="log" format="txt" label="TAREAN log file"/>
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150 <data name="ReportArchive" format="zip" label="TAREAN Archive with HTML report from data ${FastaFile.hid}"/>
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151 <data name="ReportFile" format="html" label="TAREAN HTML report from data ${FastaFile.hid}"/>
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152 </outputs>
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153
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154 <help>
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155 **HELP**
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156
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157 TAREAN - TAndem REpeat ANalyzer is a computational pipeline for
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158 **unsupervised identification of satellite repeats** from unassembled
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159 sequence reads. The pipeline uses low-pass paired-end whole genome
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160 sequence reads and performs graph-based clustering. The resulting
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161 clusters, representing all types of repeats present in the genome, are
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162 then examined to identify those containing circular structures indicative
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163 of tandem repeats. A poster summarizing TAREAN principles and
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164 implementation can be found `here.`__
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165
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166
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167 .. __: http://w3lamc.umbr.cas.cz/lamc/?page_id=312
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168
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169 **Input data**
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170
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171
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172 The analysis requires **paired-end reads** generated by whole genome
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173 shotgun sequencing. The data should be provided as a single input file in
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174 fasta format with the reads interlaced (see example below). All the pairs
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175 must be complete, i.e. both "forward" and "reverse" sequence reads must be
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176 present. The reads should all be trimmed to the same length. The optimal
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177 size range is between 100 and 200 nucleotides. The number of reads to be
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178 analyzed should not exceed 1x coverage of the genome. Genome coverage
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179 between 0.01 and 0.5x is recommended. The reads should be filtered for
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180 quality. The recommended quality filtering is as follows: each read should
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181 have a quality score >=10 for 95% of the bases, i.e. if your reads are 100
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182 base pairs long, then a read only passes this quality threshold if 95
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183 bases have a quality of 10 or higher. Additionally, any reads containing
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184 indeterminate base pairs (indicated as N in the reads) should be removed.
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185 Finally, if either one of the reads in a pair fails to meet the
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186 aforementioned thresholds, **both** sequences should be removed.
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187 example of interlaced input format::
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188
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189 >0001_f
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190 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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191 >0001_r
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192 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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193 >0002_f
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194 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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195 >0002_r
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196 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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197 >0003_f
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198 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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199 >0003_r
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200 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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201 ...
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202
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203
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204 To perform the quality filtering on your fastQ formatted data as described
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205 above, and to interlace your paired-end sequence reads,
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206 please use the `Preprocessing of paired-reads`__ tool.
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207
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208 .. __: tool_runner?tool_id=paired_fastq_filtering
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209
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210
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211 **Additional parameters**
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212
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213 **Sample size** defines how many reads will be used during the computation.
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214 The default setting of 500,000 reads will enable detection of high copy
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215 number satellites within several hours. For higher
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216 sensitivity the sample size can be increased. Since the sample size affects
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217 memory usage, this parameter may be automatically adjusted to a lower value
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218 during the run. The maximum sample size which can be processed depends on the
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219 repetitiveness of the analyzed genome. This significantly limits the number of reads
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220 that can be analyzed with the TAREAN pipeline.
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221
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222 **Perform cluster merging**. Families of repetitive elements are
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223 frequently split into multiple clusters rather than being represented as a
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224 single one. If you do not want to merge clusters based on the presence
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225 of broken read pairs, disable this option.
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226
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227 **Use custom repeat database**. This option allows users to perform similarity
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228 comparison of identified repeats to their custom databases. The repeat class should
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229 be encoded in FASTA headers of database entries in order to allow correct
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230 parsing of similarity hits.
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231
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232 **Similarity search options** By default sequence reads are compared using
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233 mgblast program. Default threshold is explicitly set to 90% sequence
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234 similarity spanning at least 55% of the read length (in the case of reads
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235 differing in length it applies to the longer one). Additionally, sequence
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236 overlap must be at least 55 nt. If you select option for shorter reads
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237 than 100 nt, minimum overlap 55 nt is not required.
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238
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239 By default,
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240 mgblast search use DUST program to filter out
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241 low-complexity sequences. If you want
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242 to increase sensitivity of detection of satellites with shorter monomer
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243 use option with '*no masking of low complexity repeats*'. Note that omitting
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244 DUST filtering will significantly increase running times
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245
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246 **Output**
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247
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248 A list of clusters identified as putative satellite repeats, their genomic
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249 abundance and various cluster characteristics are provided. Length and
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250 consensus sequences of reconstructed monomers are also shown and
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251 accompanied by a detailed output from kmer-based reconstruction including
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252 sequences and sequence logos of alternative variants of monomer sequences.
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253
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254 The output includes an **HTML summary** with a table listing all analyzed
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255 clusters. More detailed information about clusters is provided in
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256 additional files and directories. All results are also provided as a
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257 downloadable **zip archive**. Since read clustering results in
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258 thousands of clusters, the search for satellite repeats is limited to
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259 a subset of the largest ones corresponding to the most abundant genomic
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260 repeats. The default setting of the pipeline is to analyze all clusters containing at least
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261 0.01% of the input reads. Besides the satellite repeats, three other
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262 groups of clusters are reported in the output (1) LTR-retrotransposons,
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263 (2) 45S and 5S rDNA and (3) all remaining clusters passing the size
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264 threshold. As (1) and (2) contain sequences with circular
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265 graphs, their consensus is calculated in the same way as for satellite
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266 repeats. Additionally a **log file** reporting the progress of the
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267 computational pipeline is provided.
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268
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269
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270 </help>
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271
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272 </tool>
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