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planemo upload for repository https://github.com/phac-nml/refseq_masher commit e83730c5df84a960af58ff09db7eb09d11df2398
author nml
date Wed, 08 May 2019 09:15:56 -0400
parents 26df66c32861
children 1ec42f033bb4
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2c1cb37a3ffe planemo upload for repository https://github.com/phac-nml/refseq_masher commit e83730c5df84a960af58ff09db7eb09d11df2398
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1 <tool id="refseq_masher_contains" name="RefSeq Masher Contains" version="0.1.2">
0
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2 <description>
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3 Find NCBI RefSeq Genomes contained in your sequences
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.1.1">refseq_masher</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10
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11 #import re
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12 #import os
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13
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14 #if $input.type == 'fasta'
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15 #set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0])
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16 ln -s "$input.fasta" $input_files &&
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17 #elif $input.type == 'paired'
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18 #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.forward.name) else '.fastq'
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19 #set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext)
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20 #set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq'
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21 #set $_reverse = '"{}_2{}"'.format($re.sub(r'_[12]\..+$', '', $input.reverse.name), $_reverse_ext)
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22 #set $input_files = '{} {}'.format($_forward, $_reverse)
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23 ln -s "$input.forward" $_forward &&
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24 ln -s "$input.reverse" $_reverse &&
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25 #elif $input.type == 'single'
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26 #set $input_files = '"{}"'.format($input.single.name)
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27 ln -s "$input.single" $input_files &&
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28 #elif $input.type == 'paired_collection'
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29 #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.forward)) else '.fastq'
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30 #set $_forward = '"{}_1{}"'.format($input.paired_collection.name, $_forward_ext)
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31 #set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.reverse)) else '.fastq'
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32 #set $_reverse = '"{}_2{}"'.format($input.paired_collection.name, $_reverse_ext)
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33 #set $input_files = '{} {}'.format($_forward, $_reverse)
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34 ln -s "$input.paired_collection.forward" $_forward &&
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35 ln -s "$input.paired_collection.reverse" $_reverse &&
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36 #end if
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37
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38 refseq_masher
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39 $adv.verbosity
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40 contains
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41 --output refseq_masher-contains.${adv.output_type}
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42 --output-type $adv.output_type
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43 --top-n-results $adv.top_n_results
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44 --parallelism "\${GALAXY_SLOTS:-1}"
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45 --min-identity $adv.min_identity
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46 --max-pvalue $adv.max_pvalue
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47 $input_files
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48
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49 ]]>
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50 </command>
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51 <inputs>
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52 <conditional name="input">
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53 <param name="type" type="select" label="Sequence input type">
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54 <option value="fasta">FASTA</option>
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55 <option value="paired">Paired-end FASTQs</option>
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56 <option value="single">Single-end FASTQ</option>
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57 <option value="paired_collection">Paired-end FASTQ collection</option>
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58 </param>
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59 <when value="fasta">
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60 <param name="fasta"
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61 type="data" format="fasta"
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62 optional="false"
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63 label="FASTA file"
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64 />
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65 </when>
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66 <when value="paired">
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67 <param name="forward"
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68 type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"
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69 optional="false"
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70 label="Forward FASTQ file"
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71 help="Must have ASCII encoded quality scores"
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72 />
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73 <param name="reverse"
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74 type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"
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75 optional="false"
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76 label="Reverse FASTQ file"
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77 help="File format must match the Forward FASTQ file"
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78 />
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79 </when>
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80 <when value="single">
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81 <param name="single"
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82 type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"
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83 optional="false"
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84 label="Single-end FASTQ file"
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85 />
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86 </when>
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87 <when value="paired_collection">
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88 <param name="paired_collection"
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89 type="data_collection" format="fastq,fastqsanger,fastqillumina,fastqsolexa,fastq.gz,txt"
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90 collection_type="paired"
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91 optional="false"
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92 label="Paired-end FASTQ collection"
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93 help=""
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94 />
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95 </when>
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96 </conditional>
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97 <section name="adv" title="Advanced Options" expanded="false">
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98 <param name="top_n_results"
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99 type="integer"
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100 label="Top N matches to report (0 to report all)"
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101 min="0"
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102 value="0"
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103 optional="true"
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104 />
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105 <param name="min_identity"
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106 type="float" value="0.9" min="0.0" max="1.0"
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107 label="Mash dist min. identity to report"
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108 optional="true"
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109 />
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110 <param name="max_pvalue"
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111 type="float" value="0.01" min="0.0" max="1.0"
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112 label="Mash screen max. p-value to report"
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113 optional="true"
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114 />
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115 <param name="output_type"
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116 type="select"
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117 label="Output type"
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118 multiple="false">
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119 <option value="tab" selected="true">Tabular (tab-delimited values)</option>
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120 <option value="csv">CSV (Comma Separated Values)</option>
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121 </param>
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122 <param name="verbosity"
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123 type="select"
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124 label="Logging verbosity">
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125 <option value="">Error messages only</option>
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126 <option value="-v">Show warning messages</option>
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127 <option value="-vv" selected="true">Show info messages</option>
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128 <option value="-vvv">Show debug messages</option>
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129 </param>
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130 </section>
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131 </inputs>
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132 <outputs>
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133 <data
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134 name="output_path_csv"
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135 format="csv"
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136 label="RefSeq Masher contains table"
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137 from_work_dir="refseq_masher-contains.csv">
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138 <filter>adv['output_type'] == 'csv'</filter>
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139 </data>
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140 <data
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141 name="output_path_tab"
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142 format="tabular"
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143 label="RefSeq Masher contains table"
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144 from_work_dir="refseq_masher-contains.tab">
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145 <filter>adv['output_type'] == 'tab'</filter>
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146 </data>
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147 </outputs>
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148 <tests>
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149 <test>
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150 <conditional name="input">
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151 <param name="type" value="single"/>
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152 <param name="single" value="SRR1203042_1-head4000.fastq"/>
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153 </conditional>
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154 <section name="adv">
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155 <param name="top_n_results" value="5"/>
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156 <param name="output_type" value="tab"/>
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157 <param name="min_identity" value="0.9"/>
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158 <param name="max_pvalue" value="0.01"/>
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159 </section>
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160 <output name="output_path_tab"
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161 value="SRR1203042_1-head4000-contains.tab"
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162 ftype="tabular"
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163 lines_diff="0">
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164 </output>
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165 </test>
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166 </tests>
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167 <help>
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168 <![CDATA[
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169 RefSeq Masher - Containment
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170 ===========================
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171
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172 Find what NCBI RefSeq genomes are contained within your sequence data using Mash_ with a Mash sketch database of 54,925 NCBI RefSeq Genomes.
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173
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174
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175 Source code available on Github at github.com/phac-nml/refseq_masher
0
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176
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177
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178 `contains` - find what NCBI RefSeq Genomes are contained in your input sequences
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179 --------------------------------------------------------------------------------
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180
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181 If you have a metagenomic sample or maybe a sample with some contamination, you may be interested in seeing what's in your sample. You can do this with `refseq_masher contains <INPUT>`.::
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182
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183 Usage: refseq_masher contains [OPTIONS] INPUT...
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184
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185 Find the NCBI RefSeq genomes contained in your sequence files using Mash
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186 Screen
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187
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188 Input is expected to be one or more FASTA/FASTQ files or one or more
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189 directories containing FASTA/FASTQ files. Files can be Gzipped.
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190
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191 Options:
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192 --mash-bin TEXT Mash binary path (default="mash")
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193 -o, --output PATH Output file path (default="-"/stdout)
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194 --output-type [tab|csv] Output file type (tab|csv)
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195 -n, --top-n-results INTEGER Output top N results sorted by identity in
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196 ascending order (default=0/all)
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197 -i, --min-identity FLOAT Mash screen min identity to report
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198 (default=0.9)
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199 -v, --max-pvalue FLOAT Mash screen max p-value to report
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200 (default=0.01)
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201 -p, --parallelism INTEGER Mash screen parallelism; number of threads to
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202 spawn (default=1)
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203 -h, --help Show this message and exit.
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204
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205
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206 Example - metagenomic a sample SAMEA1877340_
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207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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208
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209 For this example, we're going to see what RefSeq genomes are contained within sample SAMEA1877340_ from BioProject PRJEB1775_.
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210
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211
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212 Description from BioProject PRJEB1775_:
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213
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214 .. epigraph::
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215
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216 Design, Setting and Patients Forty-five samples were selected from a set of fecal specimens obtained from patients with diarrhea during the 2011 outbreak of STEC O104:H4 in Germany. Samples were chosen to represent STEC-positive patients with a range of clinical conditions and colony counts together with a small number of patients with other infections (Campylobacter jejnuni, Clostridium difficile and Salmonella enterica). Samples were subjected to high-throughput sequencing on the Illumina MiSeq and HiSeq 2500, followed by bioinformatics analysis.
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217
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218
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219 We're going to download the FASTQ files for ERR260489_::
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220
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221 wget ftp.sra.ebi.ac.uk/vol1/fastq/ERR260/ERR260489/ERR260489_1.fastq.gz
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222 wget ftp.sra.ebi.ac.uk/vol1/fastq/ERR260/ERR260489/ERR260489_2.fastq.gz
0
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223
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224
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225 We're going to run `refseq_masher` against these FASTQ files::
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226
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227 refseq_masher -vv contains --top-n-results 50 -p 12 -o containment-ERR260489.tab ERR260489_1.fastq.gz ERR260489_2.fastq.gz
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228
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229 **Log**::
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230
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231 2018-01-29 10:59:25,849 INFO: Grouped 2 fastqs into 1 groups [in ...refseq_masher/refseq_masher/utils.py:174]
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232 2018-01-29 10:59:25,849 INFO: Collected 0 FASTA inputs and 1 read sets [in ...refseq_masher/refseq_masher/utils.py:185]
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233 2018-01-29 10:59:25,849 INFO: Running Mash Screen with NCBI RefSeq sketch database against sample "ERR260489" with inputs: ['../ERR260489_1.fastq.gz', '../ERR260489_2.fastq.gz'] [in ...refseq_masher/refseq_masher/mash/screen.py:44]
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234 Loading ...refseq_masher/refseq_masher/data/RefSeqSketches.msh...
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235 4669418 distinct hashes.
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236 Streaming from 2 inputs...
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237 Estimated distinct k-mers in pool: 206836855
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238 Summing shared...
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239 Computing coverage medians...
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240 Writing output...
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241 2018-01-29 11:00:19,665 INFO: Ran Mash Screen on all input. Merging NCBI taxonomic information into results output. [in ...refseq_masher/refseq_masher/cli.py:134]
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242 2018-01-29 11:00:19,666 INFO: Fetching all taxonomy info for 23 unique NCBI Taxonomy UIDs [in ...refseq_masher/refseq_masher/taxonomy.py:35]
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243 2018-01-29 11:00:19,669 INFO: Dropping columns with all NA values (ncol=32) [in ...refseq_masher/refseq_masher/taxonomy.py:38]
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244 2018-01-29 11:00:19,671 INFO: Columns with all NA values dropped (ncol=12) [in ...refseq_masher/refseq_masher/taxonomy.py:40]
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245 2018-01-29 11:00:19,671 INFO: Merging Mash results with relevant taxonomic information [in ...refseq_masher/refseq_masher/taxonomy.py:41]
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246 2018-01-29 11:00:19,674 INFO: Merged Mash results with taxonomy info [in ...refseq_masher/refseq_masher/taxonomy.py:43]
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247 2018-01-29 11:00:19,674 INFO: Merged taxonomic information into results output [in ...refseq_masher/refseq_masher/cli.py:136]
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248 2018-01-29 11:00:19,674 INFO: Reordering output columns [in ...refseq_masher/refseq_masher/cli.py:137]
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249 2018-01-29 11:00:19,677 INFO: Wrote output to "containment-ERR260489.tab" [in ...refseq_masher/refseq_masher/writers.py:20]
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250
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251
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252
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253 **Output**
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254
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255 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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256 | sample | top_taxonomy_name | identity | shared_hashes | median_multiplicity | pvalue | full_taxonomy | taxonomic_subspecies | taxonomic_species | taxonomic_genus | taxonomic_family | taxonomic_order | taxonomic_class | taxonomic_phylum | taxonomic_superkingdom | subspecies | serovar | plasmid | bioproject | biosample | taxid | assembly_accession | match_id | taxonomic_species group | match_comment |
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257 +===========+======================================+==========+================+======================+========+==================================================================================================================================================+=======================+==============================+==================+====================+==================+=====================+===================+=========================+============+=========+==========+============+===========+=========+=====================+==============================================================================================+==========================+================+
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258 | ERR260489 | Bacteroides fragilis | 1.0 | 400/400 | 786 | 0.0 | Bacteria; FCB group; Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; fragilis | | Bacteroides fragilis | Bacteroides | Bacteroidaceae | Bacteroidales | Bacteroidia | Bacteroidetes | Bacteria | | | pLV22a | | | 817 | | ./rcn/refseq-NG-817-.-.-.-pLV22a-Bacteroides_fragilis.fna | | |
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259 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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260 | [1 row] | | | | | | | | | | | | | | | | | | | | | | | | |
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261 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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262 | ERR260489 | Escherichia coli O104:H4 str. E92/11 | 1.0 | 400/400 | 48 | 0.0 | Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia; coli; O104:H4; str. E92/11 | | Escherichia coli | Escherichia | Enterobacteriaceae | Enterobacterales | Gammaproteobacteria | Proteobacteria | Bacteria | | | pE9211p3 | | | 1090927 | NZ_AHAU | ./rcn/refseq-NZ-1090927-.-.-NZ_AHAU-pE9211p3-Escherichia_coli_O104_H4_str._E92_11.fna | | |
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263 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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264 | [3 rows] | | | | | | | | | | | | | | | | | | | | | | | | |
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265 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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266 | ERR260489 | Kingella kingae KKC2005004457 | 1.0 | 400/400 | 5 | 0.0 | Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Kingella; kingae; KKC2005004457 | | Kingella kingae | Kingella | Neisseriaceae | Neisseriales | Betaproteobacteria | Proteobacteria | Bacteria | | | unnamed | | | 1229911 | | ./rcn/refseq-NG-1229911-.-.-.-unnamed-Kingella_kingae_KKC2005004457.fna | | |
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267 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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268 | ERR260489 | Bacteroides cellulosilyticus WH2 | 0.99984 | 399/400 | 772 | 0.0 | Bacteria; FCB group; Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; cellulosilyticus; WH2 | | Bacteroides cellulosilyticus | Bacteroides | Bacteroidaceae | Bacteroidales | Bacteroidia | Bacteroidetes | Bacteria | | | pBWH2B | | | 1268240 | NZ_ATFI | ./rcn/refseq-NZ-1268240-.-.-NZ_ATFI-pBWH2B-Bacteroides_cellulosilyticus_WH2.fna | | |
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269 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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270 | [1 row] | | | | | | | | | | | | | | | | | | | | | | | | |
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271 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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272 | ERR260489 | Klebsiella pneumoniae | 0.99984 | 399/400 | 4 | 0.0 | Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Klebsiella; pneumoniae | | Klebsiella pneumoniae | Klebsiella | Enterobacteriaceae | Enterobacterales | Gammaproteobacteria | Proteobacteria | Bacteria | | | pMRC151 | | | 573 | | ./rcn/refseq-NG-573-.-.-.-pMRC151-Klebsiella_pneumoniae.fna | | |
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273 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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274 | [37 rows] | | | | | | | | | | | | | | | | | | | | | | | | |
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275 +-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+
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276
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277 Some of the top genomes contained in this sample are sorted by identity and median multiplicity are:
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278
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279 - *Bacteroides fragilis* - fully contained (400/400) and high multiplicity (768)
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280 - *Escherichia coli* O104:H4 - fully contained (400/400) and median multiplicity of 48
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281 - *Kingella kingae* - fully contained (400/400) and median multiplicity of 5
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282 - *Klebsiella pneumoniae* - 399/400 sketches contained with median multiplicity of 4
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283
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284 So with Mash we are able to find that the sample contained the expected genomic data (especially *E. coli* O104:H4).
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285
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286
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287
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288 Legal
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289 -----
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290
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291 Copyright Government of Canada 2017
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292
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293 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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294
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295 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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296 this work except in compliance with the License. You may obtain a copy of the
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297 License at:
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298
1
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299 www.apache.org/licenses/LICENSE-2.0
0
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300
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301 Unless required by applicable law or agreed to in writing, software distributed
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302 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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303 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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304 specific language governing permissions and limitations under the License.
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305
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306 Contact
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307 -------
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308
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309 **Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca
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310
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311
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312
1
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313 .. _Mash: genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
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314 .. _SAMEA1877340: www.ebi.ac.uk/ena/data/view/SAMEA1877340
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315 .. _PRJEB1775: www.ebi.ac.uk/ena/data/view/PRJEB1775
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316 .. _ERR260489: www.ebi.ac.uk/ena/data/view/ERR260489&display=html
0
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317
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318 ]]>
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319 </help>
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320 <citations>
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321 <!-- Citation for Mash paper -->
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322 <citation type="doi">10.1186/s13059-016-0997-x</citation>
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323 </citations>
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324 </tool>