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annotate salsa2.xml @ 4:41c4e48b0617 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 41b8952cd0739db0b5eb62d5dd9ccc7bc0f1925f
author iuc
date Thu, 19 May 2022 14:16:51 +0000
parents 5af503c47367
children d6713454590c
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1 <tool id="salsa" name="SALSA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>scaffold long read assemblies with Hi-C</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.3</token>
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5 <token name="@VERSION_SUFFIX@">3</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">SALSA</xref>
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9 </xrefs>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement>
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12 <requirement type="package" version="1.11">samtools</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
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15 ln -s '$fasta_in' input.fasta &&
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16 samtools faidx input.fasta &&
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17
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18 run_pipeline.py
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19 -a '$fasta_in'
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20 -l input.fasta.fai
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21 #if $enzyme_conditional.enzyme_options == 'preconfigured':
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22 #if $enzyme_conditional.preconfigured_enzymes == 'dovetail'
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23 -e 'GATC'
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24 #else if $enzyme_conditional.preconfigured_enzymes == 'arima1'
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25 -e 'GATC,GANTC'
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26 #else
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27 -e 'GATC,GANTC,CTNAG,TTAA'
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28 #end if
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29 #else:
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30 -e '${enzyme_conditional.manual_enzyme}'
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31 #end if
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32 -b '$bed_file'
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33 #if str($cutoff):
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34 -c '$cutoff'
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35 #end if
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36 #if $gfa_file:
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37 -g '$gfa_file'
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38 #end if
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39 #if $iter:
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40 -i '$iter'
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41 #end if
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42 #if $gensize:
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43 -s '$gensize'
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44 #end if
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45 -m '$clean'
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46 -o ./out
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47 ]]></command>
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48 <inputs>
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49 <param name="fasta_in" type="data" format="fasta" label="Initial assembly file" help="Headers must not contain ':'."/>
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50 <param name="bed_file" type="data" format="bed" label="Bed alignment" help="To start scaffolding with SALSA, reads need to be mapped to the assembly.
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51 BWA or BOWTIE2 are recommended. SALSA requires a bed file as the input. The alignment bam file can be converted using the bamToBed command from
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52 the Bedtools package."/>
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53 <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold"/>
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54 <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs"
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55 help="An assembly graph can be optionally provided to guide the scaffolding, potentially reducing the scaffolding errors"/>
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56 <conditional name="enzyme_conditional">
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57 <param name="enzyme_options" type="select" label="Enzyme selection" help="Hi-C experiments can use different restriction enzymes.
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58 The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual
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59 sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you
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60 use an enzyme-free prep, e.g. Omin-C.">
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61 <option value="preconfigured">Preconfigured restriction enzymes</option>
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62 <option value="specific">Enter a specific sequence</option>
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63 </param>
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64 <when value="preconfigured">
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65 <param name="preconfigured_enzymes" type="select" multiple="true" label="Preconfigured enzymes">
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66 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
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67 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
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68 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
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69 </param>
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70 </when>
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71 <when value="specific">
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72 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
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73 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
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74 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
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75 </param>
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76 </when>
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77 </conditional>
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78 <param name="iter" argument="-i" type="integer" min="0" max="20" label="Iterations" optional="true"
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79 help="SALSA will scaffold through sequential iterations. The default number of iterations is 3. Increasing the number of iterations will
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80 potentially increase the number of joins, however it could also introduce additional misjoins"/>
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81 <param name="clean" argument="-m" type="boolean" label="Clean Assembly" checked="false" truevalue='yes' falsevalue="no" help="Set this option to 'yes' if you want to find misassemblies in input assembly" />
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82 <param name="gensize" argument="-s" type="integer" label="Expected Genome Size" optional="true" help="Expected Genome size of the assembled genome. If not set, Salsa will estimate genome size." />
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83 </inputs>
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84 <outputs>
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85 <data name="scaffolds_fasta" format="fasta" from_work_dir="out/scaffolds_FINAL.fasta" label="${tool.name} on ${on_string}: FASTA assembly"/>
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86 <data name="scaffolds_agp" format="tabular" from_work_dir="out/scaffolds_FINAL.agp" label="${tool.name} on ${on_string}: agp output"/>
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="fasta_in" value="test.fasta"/>
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91 <param name="length" value="test.fai"/>
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92 <param name="bed_file" value="test.bed"/>
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93 <param name="gfa_file" value="test.gfa1"/>
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94 <conditional name="enzyme_conditional">
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95 <param name="enzyme_options" value="specific"/>
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96 <param name="manual_enzyme" value="GATC,GANTC"/>
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97 </conditional>
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98 <param name="enzyme" value="GATC,GANTC"/>
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99 <param name="cutoff" value="1000"/>
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100 <param name="iter" value="3"/>
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101 <param name="clean" value="yes"/>
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102 <output name="scaffolds_fasta" file="out.fasta"/>
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103 <output name="scaffolds_agp" file="out.agp"/>
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104 </test>
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105 <!--Test manual enzyme-->
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106 <test>
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107 <param name="fasta_in" value="test.fasta"/>
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108 <param name="bed_file" value="test.bed"/>
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109 <param name="gfa_file" value="test.gfa1"/>
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110 <conditional name="enzyme_conditional">
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111 <param name="enzyme_options" value="specific"/>
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112 <param name="manual_enzyme" value="GATC,GANTC"/>
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113 </conditional>
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114 <param name="cutoff" value="1000"/>
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115 <param name="iter" value="3"/>
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116 <param name="clean" value="yes"/>
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117 <output name="scaffolds_fasta" file="out.fasta"/>
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118 <output name="scaffolds_agp" file="out.agp"/>
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119 </test>
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120 <!--Test predefined enzyme-->
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121 <test>
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122 <param name="fasta_in" value="test.fasta"/>
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123 <param name="bed_file" value="test.bed"/>
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124 <param name="gfa_file" value="test.gfa1"/>
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125 <conditional name="enzyme_conditional">
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126 <param name="enzyme_options" value="preconfigured"/>
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127 <param name="preconfigured_enzymes" value="arima1"/>
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128 </conditional>
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129 <param name="cutoff" value="1000"/>
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130 <param name="iter" value="3"/>
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131 <param name="clean" value="yes"/>
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132 <output name="scaffolds_fasta" file="out.fasta"/>
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133 <output name="scaffolds_agp" file="out.agp"/>
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134 </test>
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135 </tests>
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136 <help><![CDATA[
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137 .. class:: infomark
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138
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139 **Purpose**
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140
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141 SALSA (Simple AssembLy ScAffolder) is a scaffolding tool based on a computational method that exploits the genomic proximity
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142 information in Hi-C data sets for long range scaffolding of de novo genome assemblies.
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143
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144 ----
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145
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146 .. class:: infomark
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147
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148 **Mapping reads**
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149
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150 To start the scaffolding, first step is to map reads to the assembly. We recommend using `BWA <https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2>`_
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151 or `BOWTIE2 <https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0>`_ aligner to map reads. The read mapping generates a bam file. SALSA requires
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152 BED file as the input. This can be done using the bamToBed command from the `Bedtools package <http://bedtools.readthedocs.io/en/latest/>`_. Also, SALSA requires BED files to be sorted by the
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153 read name, rather than the alignment coordinates. Once you have bam file, you can run following commands to get the bam file needed as an input to SALSA.
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154
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155 Since Hi-C reads and alignments contain experimental artifacts, the alignments needs some postprocessing. To align and postprocess
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156 the alignments, you can use the pipeline released by Arima Genomics which can be found in the `GitHub repository <https://github.com/ArimaGenomics>`_.
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157
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158 Additional information on how to generate/filter the bam `here <https://github.com/marbl/SALSA#mapping-reads>`_.
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159
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160 ]]></help>
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161 <citations>
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162 <citation type="doi">10.1101/261149</citation>
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163 <citation type="doi">10.1186/s12864-017-3879-z</citation>
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164 </citations>
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165 </tool>