rulegraph_simple.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<g id="clust1" class="cluster">
<title>cluster_0</title>
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<text text-anchor="middle" x="96" y="-490" font-family="sans" font-size="10.00">Input</text>
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<g id="clust2" class="cluster">
<title>cluster_1</title>
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<text text-anchor="middle" x="243" y="-415" font-family="sans" font-size="10.00">Preprocess</text>
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<title>cluster_2</title>
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<text text-anchor="middle" x="439" y="-415" font-family="sans" font-size="10.00">Assemble</text>
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<title>cluster_3</title>
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<text text-anchor="middle" x="786" y="-525" font-family="sans" font-size="10.00">Prokaryotes</text>
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<g id="clust6" class="cluster">
<title>cluster_3_1</title>
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<text text-anchor="middle" x="590.5" y="-496" font-family="sans" font-size="10.00">Cluster</text>
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<g id="clust7" class="cluster">
<title>cluster_3_2</title>
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<text text-anchor="middle" x="988.25" y="-415" font-family="sans" font-size="10.00">Quantify</text>
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<g id="clust8" class="cluster">
<title>cluster_3_3</title>
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<text text-anchor="middle" x="788.25" y="-469" font-family="sans" font-size="10.00">Annotate</text>
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<title>cluster_4</title>
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<text text-anchor="middle" x="787" y="-303" font-family="sans" font-size="10.00">Viruses</text>
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<g id="clust10" class="cluster">
<title>cluster_4_1</title>
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<text text-anchor="middle" x="640.5" y="-220" font-family="sans" font-size="10.00">Cluster</text>
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<g id="clust11" class="cluster">
<title>cluster_4_2</title>
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<text text-anchor="middle" x="889.75" y="-81" font-family="sans" font-size="10.00">Quantify</text>
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<g id="clust12" class="cluster">
<title>cluster_4_3</title>
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<text text-anchor="middle" x="936.5" y="-274" font-family="sans" font-size="10.00">Annotate</text>
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<!-- reference -->
<g id="node1" class="node">
<title>reference</title>
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<text text-anchor="middle" x="141" y="-458" font-family="sans" font-size="10.00">Reference</text>
<text text-anchor="middle" x="141" y="-447" font-family="sans" font-size="10.00">Genome</text>
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<!-- bowtie2 -->
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<title>bowtie2</title>
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<text text-anchor="middle" x="242" y="-383" font-family="sans" font-size="10.00">bowtie2</text>
<text text-anchor="middle" x="242" y="-372" font-family="sans" font-size="10.00">Host</text>
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<!-- reference&#45;&gt;bowtie2 -->
<g id="edge18" class="edge">
<title>reference&#45;&gt;bowtie2</title>
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<!-- fastq -->
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<title>fastq</title>
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<text text-anchor="middle" x="45" y="-458" font-family="sans" font-size="10.00">FASTQ</text>
<text text-anchor="middle" x="45" y="-447" font-family="sans" font-size="10.00">reads</text>
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<!-- fastp -->
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<title>fastp</title>
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<!-- fastq&#45;&gt;fastp -->
<g id="edge19" class="edge">
<title>fastq&#45;&gt;fastp</title>
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<!-- extract -->
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<title>extract</title>
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<text text-anchor="middle" x="341" y="-383" font-family="sans" font-size="10.00">Extract</text>
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<!-- bowtie2&#45;&gt;extract -->
<g id="edge5" class="edge">
<title>bowtie2&#45;&gt;extract</title>
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<!-- extract&#45;&gt;bowtie2 -->
<g id="edge6" class="edge">
<title>extract&#45;&gt;bowtie2</title>
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<!-- megahit -->
<g id="node9" class="node">
<title>megahit</title>
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<text text-anchor="middle" x="439" y="-377.5" font-family="sans" font-size="10.00">MEGAHIT</text>
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<!-- extract&#45;&gt;megahit -->
<g id="edge20" class="edge">
<title>extract&#45;&gt;megahit</title>
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<!-- fastp&#45;&gt;bowtie2 -->
<g id="edge1" class="edge">
<title>fastp&#45;&gt;bowtie2</title>
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<!-- nonpareil -->
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<title>nonpareil</title>
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<!-- fastp&#45;&gt;nonpareil -->
<g id="edge2" class="edge">
<title>fastp&#45;&gt;nonpareil</title>
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<!-- singlem -->
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<title>singlem</title>
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<text text-anchor="middle" x="242" y="-269.5" font-family="sans" font-size="10.00">SingleM</text>
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<!-- fastp&#45;&gt;singlem -->
<g id="edge3" class="edge">
<title>fastp&#45;&gt;singlem</title>
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<!-- kraken2 -->
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<title>kraken2</title>
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<!-- fastp&#45;&gt;kraken2 -->
<g id="edge4" class="edge">
<title>fastp&#45;&gt;kraken2</title>
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<!-- concoct -->
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<title>concoct</title>
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<text text-anchor="middle" x="541" y="-458.5" font-family="sans" font-size="10.00">CONCOCT</text>
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<!-- megahit&#45;&gt;concoct -->
<g id="edge7" class="edge">
<title>megahit&#45;&gt;concoct</title>
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<!-- maxbin2 -->
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<title>maxbin2</title>
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<!-- megahit&#45;&gt;maxbin2 -->
<g id="edge8" class="edge">
<title>megahit&#45;&gt;maxbin2</title>
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<!-- metabat2 -->
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<title>metabat2</title>
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<text text-anchor="middle" x="541" y="-350.5" font-family="sans" font-size="10.00">MetaBAT2</text>
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<!-- megahit&#45;&gt;metabat2 -->
<g id="edge9" class="edge">
<title>megahit&#45;&gt;metabat2</title>
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<!-- genomad -->
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<title>genomad</title>
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<text text-anchor="middle" x="541" y="-182.5" font-family="sans" font-size="10.00">geNomad</text>
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<!-- megahit&#45;&gt;genomad -->
<g id="edge24" class="edge">
<title>megahit&#45;&gt;genomad</title>
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<!-- magscot -->
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<title>magscot</title>
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<text text-anchor="middle" x="641.5" y="-404.5" font-family="sans" font-size="10.00">MAGScoT</text>
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<!-- concoct&#45;&gt;magscot -->
<g id="edge11" class="edge">
<title>concoct&#45;&gt;magscot</title>
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<!-- maxbin2&#45;&gt;magscot -->
<g id="edge12" class="edge">
<title>maxbin2&#45;&gt;magscot</title>
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<!-- metabat2&#45;&gt;magscot -->
<g id="edge10" class="edge">
<title>metabat2&#45;&gt;magscot</title>
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<!-- gtdbtk -->
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<title>gtdbtk</title>
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<!-- magscot&#45;&gt;gtdbtk -->
<g id="edge15" class="edge">
<title>magscot&#45;&gt;gtdbtk</title>
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<title>checkm2</title>
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<!-- magscot&#45;&gt;checkm2 -->
<g id="edge14" class="edge">
<title>magscot&#45;&gt;checkm2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M673.19,-398.46C681.58,-396.12 690.79,-393.56 699.61,-391.1"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="700.65,-394.45 709.34,-388.39 698.77,-387.7 700.65,-394.45"/>
</g>
<!-- bowtie2_drep -->
<g id="node14" class="node">
<title>bowtie2_drep</title>
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<text text-anchor="middle" x="940.5" y="-383" font-family="sans" font-size="10.00">bowtie2</text>
<text text-anchor="middle" x="940.5" y="-372" font-family="sans" font-size="10.00">MAGs</text>
</g>
<!-- coverm -->
<g id="node15" class="node">
<title>coverm</title>
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<text text-anchor="middle" x="1037" y="-377.5" font-family="sans" font-size="10.00">CoverM</text>
</g>
<!-- bowtie2_drep&#45;&gt;coverm -->
<g id="edge13" class="edge">
<title>bowtie2_drep&#45;&gt;coverm</title>
<path fill="none" stroke="grey" stroke-width="2" d="M968.58,-380C978.32,-380 989.46,-380 999.84,-380"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="999.89,-383.5 1009.89,-380 999.89,-376.5 999.89,-383.5"/>
</g>
<!-- dram -->
<g id="node17" class="node">
<title>dram</title>
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<text text-anchor="middle" x="840" y="-431.5" font-family="sans" font-size="10.00">DRAM</text>
</g>
<!-- gtdbtk&#45;&gt;dram -->
<g id="edge16" class="edge">
<title>gtdbtk&#45;&gt;dram</title>
<path fill="none" stroke="grey" stroke-width="2" d="M770.75,-434C780.77,-434 792.09,-434 802.6,-434"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="802.75,-437.5 812.75,-434 802.75,-430.5 802.75,-437.5"/>
</g>
<!-- drep -->
<g id="node19" class="node">
<title>drep</title>
<path fill="none" stroke="#61d856" stroke-width="2" d="M855,-398C855,-398 825,-398 825,-398 819,-398 813,-392 813,-386 813,-386 813,-374 813,-374 813,-368 819,-362 825,-362 825,-362 855,-362 855,-362 861,-362 867,-368 867,-374 867,-374 867,-386 867,-386 867,-392 861,-398 855,-398"/>
<text text-anchor="middle" x="840" y="-377.5" font-family="sans" font-size="10.00">dRep</text>
</g>
<!-- checkm2&#45;&gt;drep -->
<g id="edge17" class="edge">
<title>checkm2&#45;&gt;drep</title>
<path fill="none" stroke="grey" stroke-width="2" d="M771.55,-380C781.35,-380 792.34,-380 802.56,-380"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="802.84,-383.5 812.84,-380 802.84,-376.5 802.84,-383.5"/>
</g>
<!-- drep&#45;&gt;bowtie2_drep -->
<g id="edge21" class="edge">
<title>drep&#45;&gt;bowtie2_drep</title>
<path fill="none" stroke="grey" stroke-width="2" d="M867.14,-380C877.78,-380 890.3,-380 901.89,-380"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="902.21,-383.5 912.21,-380 902.21,-376.5 902.21,-383.5"/>
</g>
<!-- dedupe -->
<g id="node21" class="node">
<title>dedupe</title>
<path fill="none" stroke="green" stroke-width="2" d="M656.5,-203C656.5,-203 626.5,-203 626.5,-203 620.5,-203 614.5,-197 614.5,-191 614.5,-191 614.5,-179 614.5,-179 614.5,-173 620.5,-167 626.5,-167 626.5,-167 656.5,-167 656.5,-167 662.5,-167 668.5,-173 668.5,-179 668.5,-179 668.5,-191 668.5,-191 668.5,-197 662.5,-203 656.5,-203"/>
<text text-anchor="middle" x="641.5" y="-182.5" font-family="sans" font-size="10.00">Dedupe</text>
</g>
<!-- genomad&#45;&gt;dedupe -->
<g id="edge22" class="edge">
<title>genomad&#45;&gt;dedupe</title>
<path fill="none" stroke="grey" stroke-width="2" d="M573.17,-185C583.04,-185 594.04,-185 604.23,-185"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="604.49,-188.5 614.49,-185 604.49,-181.5 604.49,-188.5"/>
</g>
<!-- mmseqs2 -->
<g id="node22" class="node">
<title>mmseqs2</title>
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<text text-anchor="middle" x="740.5" y="-182.5" font-family="sans" font-size="10.00">MMseqs2</text>
</g>
<!-- dedupe&#45;&gt;mmseqs2 -->
<g id="edge23" class="edge">
<title>dedupe&#45;&gt;mmseqs2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M668.75,-185C677.91,-185 688.42,-185 698.5,-185"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="698.76,-188.5 708.76,-185 698.76,-181.5 698.76,-188.5"/>
</g>
<!-- bowtie2v -->
<g id="node23" class="node">
<title>bowtie2v</title>
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<text text-anchor="middle" x="840" y="-49" font-family="sans" font-size="10.00">bowtie2</text>
<text text-anchor="middle" x="840" y="-38" font-family="sans" font-size="10.00">vOTUs</text>
</g>
<!-- mmseqs2&#45;&gt;bowtie2v -->
<g id="edge26" class="edge">
<title>mmseqs2&#45;&gt;bowtie2v</title>
<path fill="none" stroke="grey" stroke-width="2" d="M752.79,-166.94C763.92,-149.35 781.6,-121.97 798,-99 804.28,-90.19 811.41,-80.79 817.95,-72.39"/>
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</g>
<!-- genomad2 -->
<g id="node25" class="node">
<title>genomad2</title>
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<text text-anchor="middle" x="840" y="-236.5" font-family="sans" font-size="10.00">geNomad</text>
</g>
<!-- mmseqs2&#45;&gt;genomad2 -->
<g id="edge30" class="edge">
<title>mmseqs2&#45;&gt;genomad2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M772.08,-201.94C780.63,-206.67 790.04,-211.88 799.04,-216.87"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="797.41,-219.97 807.86,-221.75 800.8,-213.84 797.41,-219.97"/>
</g>
<!-- quastv -->
<g id="node28" class="node">
<title>quastv</title>
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<text text-anchor="middle" x="840" y="-182.5" font-family="sans" font-size="10.00">QUAST</text>
</g>
<!-- mmseqs2&#45;&gt;quastv -->
<g id="edge31" class="edge">
<title>mmseqs2&#45;&gt;quastv</title>
<path fill="none" stroke="grey" stroke-width="2" d="M772.08,-185C781.78,-185 792.6,-185 802.66,-185"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="802.8,-188.5 812.8,-185 802.8,-181.5 802.8,-188.5"/>
</g>
<!-- checkv -->
<g id="node29" class="node">
<title>checkv</title>
<path fill="none" stroke="#2a1938" stroke-width="2" d="M855,-149C855,-149 825,-149 825,-149 819,-149 813,-143 813,-137 813,-137 813,-125 813,-125 813,-119 819,-113 825,-113 825,-113 855,-113 855,-113 861,-113 867,-119 867,-125 867,-125 867,-137 867,-137 867,-143 861,-149 855,-149"/>
<text text-anchor="middle" x="840" y="-128.5" font-family="sans" font-size="10.00">CheckV</text>
</g>
<!-- mmseqs2&#45;&gt;checkv -->
<g id="edge29" class="edge">
<title>mmseqs2&#45;&gt;checkv</title>
<path fill="none" stroke="grey" stroke-width="2" d="M772.08,-168.06C782.19,-162.46 793.51,-156.19 803.93,-150.42"/>
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</g>
<!-- covermv -->
<g id="node24" class="node">
<title>covermv</title>
<path fill="none" stroke="#56d8a9" stroke-width="2" d="M955.5,-64C955.5,-64 925.5,-64 925.5,-64 919.5,-64 913.5,-58 913.5,-52 913.5,-52 913.5,-40 913.5,-40 913.5,-34 919.5,-28 925.5,-28 925.5,-28 955.5,-28 955.5,-28 961.5,-28 967.5,-34 967.5,-40 967.5,-40 967.5,-52 967.5,-52 967.5,-58 961.5,-64 955.5,-64"/>
<text text-anchor="middle" x="940.5" y="-43.5" font-family="sans" font-size="10.00">CoverM</text>
</g>
<!-- bowtie2v&#45;&gt;covermv -->
<g id="edge25" class="edge">
<title>bowtie2v&#45;&gt;covermv</title>
<path fill="none" stroke="grey" stroke-width="2" d="M868.18,-46C878.99,-46 891.59,-46 903.17,-46"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="903.43,-49.5 913.43,-46 903.43,-42.5 903.43,-49.5"/>
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<!-- virsorter2 -->
<g id="node26" class="node">
<title>virsorter2</title>
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<text text-anchor="middle" x="940.5" y="-236.5" font-family="sans" font-size="10.00">VirSorter2</text>
</g>
<!-- genomad2&#45;&gt;virsorter2 -->
<g id="edge27" class="edge">
<title>genomad2&#45;&gt;virsorter2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M872.17,-239C880.26,-239 889.11,-239 897.66,-239"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="897.86,-242.5 907.86,-239 897.86,-235.5 897.86,-242.5"/>
</g>
<!-- dramv -->
<g id="node27" class="node">
<title>dramv</title>
<path fill="none" stroke="green" stroke-width="2" d="M1053,-257C1053,-257 1021,-257 1021,-257 1015,-257 1009,-251 1009,-245 1009,-245 1009,-233 1009,-233 1009,-227 1015,-221 1021,-221 1021,-221 1053,-221 1053,-221 1059,-221 1065,-227 1065,-233 1065,-233 1065,-245 1065,-245 1065,-251 1059,-257 1053,-257"/>
<text text-anchor="middle" x="1037" y="-236.5" font-family="sans" font-size="10.00">DRAM&#45;V</text>
</g>
<!-- virsorter2&#45;&gt;dramv -->
<g id="edge28" class="edge">
<title>virsorter2&#45;&gt;dramv</title>
<path fill="none" stroke="grey" stroke-width="2" d="M973.23,-239C981.46,-239 990.41,-239 998.89,-239"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="998.93,-242.5 1008.93,-239 998.93,-235.5 998.93,-242.5"/>
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