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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
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<!-- Generated by graphviz version 2.42.3 (20191010.1750)
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<!-- Title: snakemake_dag Pages: 1 -->
<svg width="1465pt" height="409pt"
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<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 405)">
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<title>snakemake_dag</title>
<polygon fill="white" stroke="transparent" points="-4,4 -4,-405 1460.5,-405 1460.5,4 -4,4"/>
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<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
<path fill="none" stroke="#56d873" stroke-width="2" d="M780.5,-36C780.5,-36 750.5,-36 750.5,-36 744.5,-36 738.5,-30 738.5,-24 738.5,-24 738.5,-12 738.5,-12 738.5,-6 744.5,0 750.5,0 750.5,0 780.5,0 780.5,0 786.5,0 792.5,-6 792.5,-12 792.5,-12 792.5,-24 792.5,-24 792.5,-30 786.5,-36 780.5,-36"/>
<text text-anchor="middle" x="765.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
<path fill="none" stroke="#5673d8" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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</g>
<!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge">
<title>1&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M309.24,-71.97C447.86,-55.87 646.37,-32.83 728.13,-23.34"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="728.89,-26.77 738.42,-22.14 728.09,-19.82 728.89,-26.77"/>
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</g>
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
<path fill="none" stroke="#d86e56" stroke-width="2" d="M668,-108C668,-108 355,-108 355,-108 349,-108 343,-102 343,-96 343,-96 343,-84 343,-84 343,-78 349,-72 355,-72 355,-72 668,-72 668,-72 674,-72 680,-78 680,-84 680,-84 680,-96 680,-96 680,-102 674,-108 668,-108"/>
<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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</g>
<!-- 2&#45;&gt;0 -->
<g id="edge2" class="edge">
<title>2&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M573.31,-71.97C621.91,-58.57 687.98,-40.36 728.63,-29.16"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="729.68,-32.5 738.39,-26.47 727.82,-25.75 729.68,-32.5"/>
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</g>
<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
<path fill="none" stroke="#d8bc56" stroke-width="2" d="M556.5,-252C556.5,-252 438.5,-252 438.5,-252 432.5,-252 426.5,-246 426.5,-240 426.5,-240 426.5,-228 426.5,-228 426.5,-222 432.5,-216 438.5,-216 438.5,-216 556.5,-216 556.5,-216 562.5,-216 568.5,-222 568.5,-228 568.5,-228 568.5,-240 568.5,-240 568.5,-246 562.5,-252 556.5,-252"/>
<text text-anchor="middle" x="497.5" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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</g>
<!-- 3&#45;&gt;0 -->
<g id="edge3" class="edge">
<title>3&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M529.12,-215.95C568.61,-193.87 637.19,-152.87 688.5,-108 710.51,-88.76 731.97,-63.22 746.62,-44.44"/>
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</g>
<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
<path fill="none" stroke="#d8a456" stroke-width="2" d="M700,-252C700,-252 599,-252 599,-252 593,-252 587,-246 587,-240 587,-240 587,-228 587,-228 587,-222 593,-216 599,-216 599,-216 700,-216 700,-216 706,-216 712,-222 712,-228 712,-228 712,-240 712,-240 712,-246 706,-252 700,-252"/>
<text text-anchor="middle" x="649.5" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
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</g>
<!-- 4&#45;&gt;0 -->
<g id="edge4" class="edge">
<title>4&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M682.26,-215.99C696.54,-207.05 712.3,-194.85 722.5,-180 750.73,-138.9 760.44,-80.17 763.77,-46.17"/>
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</g>
<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
<path fill="none" stroke="#d85656" stroke-width="2" d="M905,-252C905,-252 742,-252 742,-252 736,-252 730,-246 730,-240 730,-240 730,-228 730,-228 730,-222 736,-216 742,-216 742,-216 905,-216 905,-216 911,-216 917,-222 917,-228 917,-228 917,-240 917,-240 917,-246 911,-252 905,-252"/>
<text text-anchor="middle" x="823.5" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
<g id="edge5" class="edge">
<title>5&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M818.57,-215.83C815.61,-205.47 811.8,-191.99 808.5,-180 795.61,-133.13 781.12,-78.44 772.68,-46.38"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="775.99,-45.2 770.06,-36.41 769.22,-46.98 775.99,-45.2"/>
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</g>
<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1093.5,-252C1093.5,-252 947.5,-252 947.5,-252 941.5,-252 935.5,-246 935.5,-240 935.5,-240 935.5,-228 935.5,-228 935.5,-222 941.5,-216 947.5,-216 947.5,-216 1093.5,-216 1093.5,-216 1099.5,-216 1105.5,-222 1105.5,-228 1105.5,-228 1105.5,-240 1105.5,-240 1105.5,-246 1099.5,-252 1093.5,-252"/>
<text text-anchor="middle" x="1020.5" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
<g id="edge6" class="edge">
<title>6&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M938.16,-215.95C898.46,-206.3 856.28,-193.49 841.5,-180 803.34,-145.17 821.8,-118.11 798.5,-72 793.86,-62.81 788.11,-53.14 782.73,-44.62"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="785.67,-42.72 777.31,-36.21 779.79,-46.51 785.67,-42.72"/>
<g id="node8" class="node">
<title>7</title>
<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1006.5,-108C1006.5,-108 908.5,-108 908.5,-108 902.5,-108 896.5,-102 896.5,-96 896.5,-96 896.5,-84 896.5,-84 896.5,-78 902.5,-72 908.5,-72 908.5,-72 1006.5,-72 1006.5,-72 1012.5,-72 1018.5,-78 1018.5,-84 1018.5,-84 1018.5,-96 1018.5,-96 1018.5,-102 1012.5,-108 1006.5,-108"/>
<text text-anchor="middle" x="957.5" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="957.5" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
<g id="edge7" class="edge">
<title>7&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M910.53,-71.88C877.17,-59.71 833.02,-43.62 802.23,-32.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="803.32,-29.06 792.73,-28.93 800.93,-35.64 803.32,-29.06"/>
<g id="node9" class="node">
<title>8</title>
<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1210.5,-108C1210.5,-108 1114.5,-108 1114.5,-108 1108.5,-108 1102.5,-102 1102.5,-96 1102.5,-96 1102.5,-84 1102.5,-84 1102.5,-78 1108.5,-72 1114.5,-72 1114.5,-72 1210.5,-72 1210.5,-72 1216.5,-72 1222.5,-78 1222.5,-84 1222.5,-84 1222.5,-96 1222.5,-96 1222.5,-102 1216.5,-108 1210.5,-108"/>
<text text-anchor="middle" x="1162.5" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1162.5" y="-82" font-family="sans" font-size="10.00">seqmode: single_end</text>
<g id="edge8" class="edge">
<title>8&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1102.2,-78.37C1019.06,-63.71 871.68,-37.72 802.86,-25.59"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="803.35,-22.12 792.9,-23.83 802.14,-29.01 803.35,-22.12"/>
<g id="node10" class="node">
<title>9</title>
<path fill="none" stroke="#56d8a2" stroke-width="2" d="M755.5,-326.5C755.5,-326.5 627.5,-326.5 627.5,-326.5 621.5,-326.5 615.5,-320.5 615.5,-314.5 615.5,-314.5 615.5,-302.5 615.5,-302.5 615.5,-296.5 621.5,-290.5 627.5,-290.5 627.5,-290.5 755.5,-290.5 755.5,-290.5 761.5,-290.5 767.5,-296.5 767.5,-302.5 767.5,-302.5 767.5,-314.5 767.5,-314.5 767.5,-320.5 761.5,-326.5 755.5,-326.5"/>
<text text-anchor="middle" x="691.5" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
<g id="edge9" class="edge">
<title>9&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M645.52,-290.32C617.74,-279.94 582.15,-266.63 552.83,-255.68"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="553.74,-252.28 543.15,-252.06 551.29,-258.84 553.74,-252.28"/>
</g>
<!-- 9&#45;&gt;5 -->
<g id="edge13" class="edge">
<title>9&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M722.78,-290.32C740.95,-280.34 764.02,-267.67 783.49,-256.97"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="785.36,-259.94 792.44,-252.06 781.99,-253.8 785.36,-259.94"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
<path fill="none" stroke="#88d856" stroke-width="2" d="M1237,-252C1237,-252 1136,-252 1136,-252 1130,-252 1124,-246 1124,-240 1124,-240 1124,-228 1124,-228 1124,-222 1130,-216 1136,-216 1136,-216 1237,-216 1237,-216 1243,-216 1249,-222 1249,-228 1249,-228 1249,-240 1249,-240 1249,-246 1243,-252 1237,-252"/>
<text text-anchor="middle" x="1186.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 9&#45;&gt;18 -->
<g id="edge26" class="edge">
<title>9&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M767.61,-291.23C773.99,-290.06 780.35,-288.97 786.5,-288 928.12,-265.74 968.19,-276.39 1113.57,-252.03"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1114.49,-255.42 1123.76,-250.29 1113.32,-248.52 1114.49,-255.42"/>
<g id="node11" class="node">
<title>10</title>
<path fill="none" stroke="#56d88a" stroke-width="2" d="M565,-329C565,-329 450,-329 450,-329 444,-329 438,-323 438,-317 438,-317 438,-300 438,-300 438,-294 444,-288 450,-288 450,-288 565,-288 565,-288 571,-288 577,-294 577,-300 577,-300 577,-317 577,-317 577,-323 571,-329 565,-329"/>
<text text-anchor="middle" x="507.5" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="507.5" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="507.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 10&#45;&gt;3 -->
<g id="edge10" class="edge">
<title>10&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M504.77,-287.69C503.69,-279.91 502.44,-270.84 501.29,-262.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="504.72,-261.75 499.89,-252.32 497.79,-262.7 504.72,-261.75"/>
<g id="edge12" class="edge">
<title>10&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M545.93,-287.88C564.79,-278.25 587.57,-266.62 606.95,-256.72"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="608.56,-259.83 615.88,-252.17 605.38,-253.6 608.56,-259.83"/>
<g id="node12" class="node">
<title>11</title>
<path fill="none" stroke="#bed856" stroke-width="2" d="M1080.5,-326.5C1080.5,-326.5 970.5,-326.5 970.5,-326.5 964.5,-326.5 958.5,-320.5 958.5,-314.5 958.5,-314.5 958.5,-302.5 958.5,-302.5 958.5,-296.5 964.5,-290.5 970.5,-290.5 970.5,-290.5 1080.5,-290.5 1080.5,-290.5 1086.5,-290.5 1092.5,-296.5 1092.5,-302.5 1092.5,-302.5 1092.5,-314.5 1092.5,-314.5 1092.5,-320.5 1086.5,-326.5 1080.5,-326.5"/>
<text text-anchor="middle" x="1025.5" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 11&#45;&gt;4 -->
<g id="edge11" class="edge">
<title>11&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M958.46,-291.13C953.41,-290.03 948.38,-288.97 943.5,-288 848.22,-269.01 820.7,-271.51 722.24,-252.27"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="722.65,-248.78 712.16,-250.27 721.29,-255.65 722.65,-248.78"/>
</g>
<!-- 11&#45;&gt;6 -->
<g id="edge15" class="edge">
<title>11&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1024.32,-290.32C1023.74,-281.92 1023.03,-271.62 1022.37,-262.19"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.86,-261.79 1021.68,-252.06 1018.87,-262.28 1025.86,-261.79"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
<path fill="none" stroke="#59d856" stroke-width="2" d="M1362,-252C1362,-252 1279,-252 1279,-252 1273,-252 1267,-246 1267,-240 1267,-240 1267,-228 1267,-228 1267,-222 1273,-216 1279,-216 1279,-216 1362,-216 1362,-216 1368,-216 1374,-222 1374,-228 1374,-228 1374,-240 1374,-240 1374,-246 1368,-252 1362,-252"/>
<text text-anchor="middle" x="1320.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 11&#45;&gt;19 -->
<g id="edge28" class="edge">
<title>11&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1092.69,-292.13C1136.95,-281.86 1196.4,-267.78 1257.02,-252.34"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.94,-255.72 1266.76,-249.85 1256.21,-248.94 1257.94,-255.72"/>
<g id="node13" class="node">
<title>12</title>
<path fill="none" stroke="#d6d856" stroke-width="2" d="M923,-326.5C923,-326.5 808,-326.5 808,-326.5 802,-326.5 796,-320.5 796,-314.5 796,-314.5 796,-302.5 796,-302.5 796,-296.5 802,-290.5 808,-290.5 808,-290.5 923,-290.5 923,-290.5 929,-290.5 935,-296.5 935,-302.5 935,-302.5 935,-314.5 935,-314.5 935,-320.5 929,-326.5 923,-326.5"/>
<text text-anchor="middle" x="865.5" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="865.5" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
<g id="edge14" class="edge">
<title>12&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M855.55,-290.32C850.47,-281.56 844.2,-270.73 838.55,-260.97"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="841.42,-258.96 833.38,-252.06 835.37,-262.47 841.42,-258.96"/>
<g id="edge16" class="edge">
<title>12&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M902.23,-290.32C923.95,-280.16 951.64,-267.21 974.76,-256.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="976.46,-259.47 984.03,-252.06 973.49,-253.12 976.46,-259.47"/>
<g id="node14" class="node">
<title>13</title>
<path fill="none" stroke="#70d856" stroke-width="2" d="M1052,-180C1052,-180 863,-180 863,-180 857,-180 851,-174 851,-168 851,-168 851,-156 851,-156 851,-150 857,-144 863,-144 863,-144 1052,-144 1052,-144 1058,-144 1064,-150 1064,-156 1064,-156 1064,-168 1064,-168 1064,-174 1058,-180 1052,-180"/>
<text text-anchor="middle" x="957.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 13&#45;&gt;7 -->
<g id="edge17" class="edge">
<title>13&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M957.5,-143.7C957.5,-135.98 957.5,-126.71 957.5,-118.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="961,-118.1 957.5,-108.1 954,-118.1 961,-118.1"/>
<g id="node15" class="node">
<title>14</title>
<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1230.5,-180C1230.5,-180 1094.5,-180 1094.5,-180 1088.5,-180 1082.5,-174 1082.5,-168 1082.5,-168 1082.5,-156 1082.5,-156 1082.5,-150 1088.5,-144 1094.5,-144 1094.5,-144 1230.5,-144 1230.5,-144 1236.5,-144 1242.5,-150 1242.5,-156 1242.5,-156 1242.5,-168 1242.5,-168 1242.5,-174 1236.5,-180 1230.5,-180"/>
<text text-anchor="middle" x="1162.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
<g id="edge18" class="edge">
<title>14&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1112.61,-143.97C1083.85,-134.14 1047.49,-121.73 1017.21,-111.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1018.2,-108.03 1007.61,-108.11 1015.94,-114.65 1018.2,-108.03"/>
<g id="edge20" class="edge">
<title>14&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1162.5,-143.7C1162.5,-135.98 1162.5,-126.71 1162.5,-118.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1166,-118.1 1162.5,-108.1 1159,-118.1 1166,-118.1"/>
<g id="node16" class="node">
<title>15</title>
<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1444.5,-180C1444.5,-180 1272.5,-180 1272.5,-180 1266.5,-180 1260.5,-174 1260.5,-168 1260.5,-168 1260.5,-156 1260.5,-156 1260.5,-150 1266.5,-144 1272.5,-144 1272.5,-144 1444.5,-144 1444.5,-144 1450.5,-144 1456.5,-150 1456.5,-156 1456.5,-156 1456.5,-168 1456.5,-168 1456.5,-174 1450.5,-180 1444.5,-180"/>
<text text-anchor="middle" x="1358.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
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<!-- 15&#45;&gt;8 -->
<g id="edge19" class="edge">
<title>15&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1310.8,-143.97C1283.42,-134.19 1248.84,-121.84 1219.97,-111.52"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1221,-108.18 1210.41,-108.11 1218.65,-114.77 1221,-108.18"/>
<g id="node17" class="node">
<title>16</title>
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<text text-anchor="middle" x="684.5" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="684.5" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<title>16&#45;&gt;9</title>
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<title>17</title>
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<text text-anchor="middle" x="1033.5" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1033.5" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<title>17&#45;&gt;11</title>
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<title>19&#45;&gt;15</title>
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<title>20</title>
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<text text-anchor="middle" x="1253.5" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1253.5" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1253.5" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<title>20&#45;&gt;18</title>
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<title>20&#45;&gt;19</title>
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Alex Kanitz's avatar
Alex Kanitz committed
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