annotate assembly_post_processor.xml @ 39:b0ea1e985a38 draft

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date Wed, 26 Apr 2017 10:25:55 -0400
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1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.0">
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2 <description>post-processes de novo transcriptome assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_assembly_post_processor" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 AssemblyPostProcessor
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11 --transcripts '$input'
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12 --prediction_method $prediction_method_cond.prediction_method
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13 #if str($prediction_method_cond.prediction_method) == 'estscan':
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14 --score_matrices '$score_matrices'
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15 #end if
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16 #if str($options_type.options_type_selector) == 'advanced':
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17 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
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18 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
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19 --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
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20 --method '$options_type.target_gene_family_assembly_cond.method'
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21 --gap_trimming $options_type.gap_trimming
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22 #end if
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23 #if str($options_type.strand_specific) == 'yes':
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24 --strand_specific
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25 #end if
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26 #if str($options_type.dereplicate) == 'yes':
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27 --dereplicate
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28 #end if
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29 --min_length $options_type.min_length
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30 #end if
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31 --num_threads \${GALAXY_SLOTS:-4}
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32 >/dev/null
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
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37 <conditional name="prediction_method_cond">
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38 <param name="prediction_method" type="select" label="Coding regions prediction method">
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39 <option value="transdecoder" selected="true">TransDecoder</option>
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40 <option value="estscan">ESTScan</option>
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41 </param>
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42 <when value="transdecoder" />
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43 <when value="estscan">
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44 <param name="score_matrices" format="smat" type="data" label="Scores matrices"/>
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45 </when>
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46 </conditional>
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47 <conditional name="options_type">
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48 <param name="options_type_selector" type="select" label="Options configuration">
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49 <option value="basic" selected="true">Basic</option>
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50 <option value="advanced">Advanced</option>
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51 </param>
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52 <when value="basic" />
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53 <when value="advanced">
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54 <conditional name="target_gene_family_assembly_cond">
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55 <param name="target_gene_family_assembly" type="select" label="Perform targeted gene assembly?">
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56 <option value="no" selected="true">No</option>
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57 <option value="yes">Yes</option>
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58 </param>
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59 <when value="no" />
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60 <when value="yes">
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61 <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
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62 <param name="scaffold" type="select" label="Gene family scaffold">
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63 <options from_data_table="plant_tribes_scaffolds" />
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64 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
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65 </param>
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66 <param name="method" type="select" label="Protein clustering method">
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67 <option value="gfam" selected="true">GFam</option>
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68 <option value="orthofinder">OrthoFinder</option>
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69 <option value="orthomcl">OrthoMCL</option>
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70 </param>
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71 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
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72 </when>
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73 </conditional>
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74 <param name="strand_specific" type="select" label="Strand-specific assembly?">
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75 <option value="no" selected="true">No</option>
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76 <option value="yes">Yes</option>
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77 </param>
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78 <param name="dereplicate" type="select" label="Remove duplicate sequences?">
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79 <option value="no" selected="true">No</option>
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80 <option value="yes">Yes</option>
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81 </param>
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82 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
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83 </when>
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84 </conditional>
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85 </inputs>
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86 <outputs>
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87 <collection name="transcripts" type="list">
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88 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" />
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89 </collection>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="input" value="assembly.fasta" ftype="fasta" />
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94 <param name="prediction_method" value="transdecoder" />
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95 <output_collection name="transcripts" type="list">
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96 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
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97 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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98 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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99 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
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100 </output_collection>
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101 </test>
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102 <test>
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103 <param name="input" value="assembly.fasta" ftype="fasta" />
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104 <param name="prediction_method" value="transdecoder" />
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105 <param name="options_type_selector" value="advanced" />
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106 <param name="gap_trimming" value="0.1" />
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107 <param name="dereplicate" value="yes" />
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108 <param name="min_length" value="200" />
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109 <output_collection name="transcripts" type="list">
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110 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
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111 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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112 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
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113 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
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114 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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115 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
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116 </output_collection>
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117 </test>
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118 </tests>
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119 <help>
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120 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
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121 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo
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122 assembled transcripts into putative coding sequences and their corresponding amino acid translations and
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123 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been
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124 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
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125 de novo assembly.
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126
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127 -----
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128
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129 **Required options**
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130
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131 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history.
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132 * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4].
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133 * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is used to find coding regions. Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net). Matrices of some organisms are also available to download.
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134
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135 **Other options**
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136
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137 * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold. Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7].
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138
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139 * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold. Gene family identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and also available at the PlantTribes github repository (https://github.com/dePamphilis/PlantTribes/tree/master/config).
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140 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroup(s) are targeted for the localized assembly.
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141 * **Protein clustering method** - gene family scaffold protein clustering method. Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters). You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
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142 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11]. The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbone gene models. The default setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0.
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143
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144 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific. If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
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145 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
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146 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
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147
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148 </help>
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149 <citations>
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150 <expand macro="citation1" />
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151 <citation type="bibtex">
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152 @article{Honaas2016,
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153 journal = {PloS one},
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154 author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH},
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155 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},
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156 year = {2016},
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157 volume = {11},
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158 number = {1},
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159 pages = {e0146062},}
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160 </citation>
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161 <citation type="bibtex">
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162 @article{Haas2013,
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163 journal = {Nature Protocols},
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164 author = {3. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD},
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165 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis},
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166 year = {2013},
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167 volume = {8},
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168 number = {8},
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169 pages = {1494-1512},}
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170 </citation>
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171 <citation type="bibtex">
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172 @article{Iseli1999,
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173 journal = {ISMB},
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174 author = {4. Iseli C, Jongeneel CV, Bucher P},
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175 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences},
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176 year = {1999},
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177 volume = {99},
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178 pages = {138-148},
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179 url = {http://estscan.sourceforge.net},}
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180 </citation>
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181 <citation type="bibtex">
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182 @article{Huang1999,
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183 journal = {Genome Research},
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184 author = {5. Huang X, Madan A},
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185 title = {CAP3: A DNA sequence assembly program},
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