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1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.6" >
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2 <stdio>
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3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
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4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
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5 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
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6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
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7 <exit_code range="1:" level="fatal" description="Error" />
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8 </stdio>
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9 <description>Improved version or repeat discovery and characterization using graph based sequence clustering</description>
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10 <requirements>
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11 <requirement type="package" version="3.7">python</requirement>
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12 <requirement type="package" version="0.9.1" >pyrserve</requirement>
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13 <requirement type="package" version=">956" >last</requirement>
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14 <requirement type="package">mafft</requirement>
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15 <requirement type="package">imagemagick</requirement>
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16 <requirement type="package">blast</requirement>
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17 <requirement type="package">diamond</requirement>
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18 <requirement type="package">blast-legacy</requirement>
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19 <requirement type="package">r-igraph</requirement>
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20 <requirement type="package">r-data.tree</requirement>
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21 <requirement type="package">r-stringr</requirement>
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22 <requirement type="package">r-r2html</requirement>
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23 <requirement type="package">r-hwriter</requirement>
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24 <requirement type="package">r-dt</requirement>
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25 <requirement type="package">r-scales</requirement>
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26 <requirement type="package">r-plotrix</requirement>
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27 <requirement type="package">r-png</requirement>
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28 <requirement type="package">r-plyr</requirement>
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29 <requirement type="package">r-dplyr</requirement>
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30 <requirement type="package">r-optparse</requirement>
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31 <requirement type="package">r-dbi</requirement>
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32 <requirement type="package">r-rsqlite</requirement>
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33 <requirement type="package">r-rserve</requirement>
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34 <requirement type="package">bioconductor-biostrings</requirement>
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35 </requirements>
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36 <command >
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37 export PYTHONHASHSEED=0;
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38 ${__tool_directory__}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
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39
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40 #if $advanced_options.advanced:
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41 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
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42 --assembly_min $advanced_options.assembly_min_cluster_size
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43
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44 #if $advanced_options.comparative.options_comparative:
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45 --prefix_length $advanced_options.comparative.prefix_length
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46 #end if
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47
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48 #if $advanced_options.custom_library.options_custom_library:
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49 -d $advanced_options.custom_library.library extra_database
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50 #end if
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51
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52 #if $advanced_options.options.options:
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53 -opt $advanced_options.options.options
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54 #end if
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55 #end if
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56 ${FastaFile} >stdout.log 2> stderr.log ;
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57 echo "STDOUT CONTENT:" >> ${log} ;
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58 cat stdout.log >> ${log} ;
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59 echo "STDERR CONTENT:" >> ${log};
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60 cat stderr.log >> ${log} &&
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61 cd tarean_output &&
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62 zip -r ${ReportArchive}.zip * &&
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63 mv ${ReportArchive}.zip ${ReportArchive} &&
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64 cp index.html ${ReportFile} &&
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65 mkdir ${ReportFile.files_path} &&
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66 cp -r --parents libdir ${ReportFile.files_path} &&
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67 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &&
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68 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &&
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69 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &&
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70 cp *.png ${ReportFile.files_path}/ &&
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71 cp *.csv ${ReportFile.files_path}/ &&
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72 cp *.html ${ReportFile.files_path}/ &&
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73 cp *.css ${ReportFile.files_path}/ &&
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74 cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || :
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75
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76 </command>
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77 <inputs>
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78 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
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79 help="Input file must contain fasta-formatted NGS reads. If paired end reads are used, reads must be interlaced and all pairs must be complete. Example of input data format is provided in the help below. "/>
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80 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="Check if you are using pair reads and input sequences contain both read mates and left mates alternate with their right mates" />
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81
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82 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
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83 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
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84 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
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85 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
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86 <option value="METAZOA3.0" >Metazoa version 3.0</option>
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87 <option value="METAZOA2.0" >Metazoa version 2.0</option>
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88 <!-- Modify setting in config.py accordingly -->
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89 </param>
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90
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91 <conditional name="advanced_options">
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92 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
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93 <when value="false">
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94 <!-- pass -->
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95 </when>
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96 <when value="true">
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97 <conditional name="comparative">
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98 <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options when you want to compare sequences multiple groups"/>
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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="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, sequences are from individial groups distinguished by sample code which must be used as prefix for sequence name. See example below."/>
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104 </when>
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105 </conditional>
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106
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107 <conditional name="blastx">
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108 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
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109 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
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110 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
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111 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
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112 </param>
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113 </conditional>
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114
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115 <conditional name="options">
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116 <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the used input data to adjust search to differences in length and error rate">
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117 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
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118 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
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119 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option>
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120 <option value="OXFORD_NANOPORE" selected="false">
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121 Pseudo short reads simulated from Oxford Nanopore data (experimental feature)
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122 </option>
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123 </param>
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124 </conditional>
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125
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126 <conditional name="custom_library">
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127 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
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128 <when value="false">
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129 <!-- do nothing here -->
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130 </when>
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131 <when value="true">
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132 <param name="library" format="fasta" type="data" label="Custom library of repeats" help="Library of repeats as DNA sequences in fasta format. The required format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
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133 </when>
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134 </conditional>
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135 <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 at all."/>
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136 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering tries to identify the most abundant tandem repeats and remove such sequences partially from analysis. Removal of abundant tandem repeat can enable to analyze higher proportion of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
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137 <param name="keep_names" label="Keep original sequences names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default sequence are relabeled using integers. If you want to keep original names, use this option."/>
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138 <param name="assembly_min_cluster_size" type="integer" label="min cluster size for assembly" value="5" min="2" max="100"/>
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139 </when>
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140 </conditional>
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141
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142 </inputs>
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143 <outputs>
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144 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
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145 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
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146 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
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147 </outputs>
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148
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149 <help>
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150 **HELP**
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151
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152 RepeatExplorer2 clustering is a computational pipeline for unsupervised
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153 identification of repeats from unassembled sequence reads. The
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154 pipeline uses low-pass whole genome sequence reads and performs graph-based
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155 clustering. Resulting clusters, representing all types of repeats, are then
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156 examined to identify and classify into repeats groups.
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157
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158 **Input data**
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159
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160 The analysis requires either **single** or **paired-end reads** generated
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161 by whole genome shotgun sequencing provided as a single fasta-formatted file.
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162 Generally, paired-end reads provide significantly better results than single
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163 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
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164 the number of analyzed reads should represent less than 1x genome equivalent
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165 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
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166 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
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167 and no Ns allowed) and only **complete read pairs** should be submitted for
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168 analysis. When paired reads are used, input data must be **interlaced** format
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169 as fasta file:
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170
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171 example of interlaced input format::
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172
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173 >0001_f
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174 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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175 >0001_r
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176 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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177 >0002_f
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178 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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179 >0002_r
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180 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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181 >0003_f
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182 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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183 >0003_r
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184 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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185 ...
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186
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187
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188 **Comparative analysis**
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189
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190 For comparative analysis sequence names must contain code (prefix) for each group.
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191 Prefix in sequences names must be of fixed length.
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192
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193 Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB ::
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194
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195 >AA0001_f
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196 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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197 >AA0001_r
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198 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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199 >AA0002_f
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200 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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201 >AA0002_r
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202 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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203 >BB0001_f
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204 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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205 >BB0001_r
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206 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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207 >BB0002_f
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208 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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209 >BB0002_r
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210 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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211
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212
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213 To prepare quality filtered and interlaced input fasta file from fastq
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214 files, use `Preprocessing of paired-reads`__ tool.
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215
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216 .. __: tool_runner?tool_id=paired_fastq_filtering
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217
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218
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219 **Additional parameters**
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220
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221 **Sample size** defines how many reads should be used in calculation.
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222 Default setting with 500,000 reads will enable detection of high copy
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223 repeats within several hours of computation time. For higher
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224 sensitivity the sample size can be set higher. Since sample size affects
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225 the memory usage, this parameter may be automatically adjusted to lower
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226 value during the run. Maximum sample size which can be processed depends on
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227 the repetitiveness of analyzed genome.
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228
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229
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230 **Select taxon and protein domain database version (REXdb)**. Classification
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231 of transposable elements is based on the similarity to our reference database
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232 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
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233 can be obtained on `repeatexplorer.org`__. Classification
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234 system used in REXdb is described in article `Systematic survey of plant
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235 LTR-retrotransposons elucidates phylogenetic relationships of their
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236 polyprotein domains and provides a reference for element classification`__
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237 Database for Metazoa species is still under development so use it with caution.
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238
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239 .. __: http://repeatexplorer.org
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240 .. __: https://doi.org/10.1186/s13100-018-0144-1
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241
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242 **Select parameters for protein domain search** REXdb is compared with s
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243 equence clusters either using blastx or diamond aligner. Diamond program
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244 is about three time faster than blastx with word size 3.
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245
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246 **Similarity search options** By default sequence reads are compared using
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247 mgblast program. Default threshold is explicitly set to 90% sequence
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248 similarity spanning at least 55% of the read length (in the case of reads
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249 differing in length it applies to the longer one). Additionally, sequence
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250 overlap must be at least 55 nt. If you select option for shorter reads
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251 than 100 nt, minimum overlap 55 nt is not required.
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252
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253 By default,
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254 mgblast search use DUST program to filter out
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255 low-complexity sequences. If you want
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256 to increase sensitivity of detection of satellites with shorter monomer
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257 use option with '*no masking of low complexity repeats*'. Note that omitting
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258 DUST filtering will significantly increase running times
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259
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260
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261 **Automatic filtering of abundant satellite repeats** perform clustering on
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262 smaller dataset of sequence reads to detect abundant high confidence
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263 satellite repeats. If such satellites are detected, sequence reads derived
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264 from these satellites are depleted from input dataset. This step enable more
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265 sensitive detection of less abundant repeats as more reads can be used
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266 in clustering step.
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267
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268 **Use custom repeat database**. This option allows users to perform similarity
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269 comparison of identified repeats to their custom databases. The repeat class must
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270 be encoded in FASTA headers of database entries in order to allow correct
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271 parsing of similarity hits. Required format for custom database sequence name is: ::
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272
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273 >reapeatname#class/subclass
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274
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275
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276 **Output**
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277
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278 List of clusters identified as putative satellite repeats, their genomic
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279 abundance and various cluster characteristics.
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280
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281 Output includes a **HTML summary** with table listing of all analyzed
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282 clusters. More detailed information about clusters is provided in
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283 additional files and directories. All results are also provided as
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284 downloadable **zip archive**. Additionally a **log file** reporting
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285 the progress of the computational pipeline is provided.
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286
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287 </help>
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288
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289 </tool>
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