test.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
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<text text-anchor="middle" x="99" y="-15.5" font-family="sans" font-size="10.00">pipeline finished</text>
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<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
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<text text-anchor="middle" x="99" y="-112" font-family="sans" font-size="10.00">convert GFA files</text>
<text text-anchor="middle" x="99" y="-101" font-family="sans" font-size="10.00"> to FASTA for</text>
<text text-anchor="middle" x="99" y="-90" font-family="sans" font-size="10.00">haplotypes</text>
<text text-anchor="middle" x="99" y="-79" font-family="sans" font-size="10.00">1 &amp; 2</text>
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<!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge">
<title>1&#45;&gt;0</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="102.5,-46.41 99,-36.41 95.5,-46.41 102.5,-46.41"/>
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<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
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<text text-anchor="middle" x="99" y="-200" font-family="sans" font-size="10.00">run final round</text>
<text text-anchor="middle" x="99" y="-189" font-family="sans" font-size="10.00"> of hifiasm with</text>
<text text-anchor="middle" x="99" y="-178" font-family="sans" font-size="10.00"> ultra&#45;long reads</text>
<text text-anchor="middle" x="99" y="-167" font-family="sans" font-size="10.00"> as original SUP reads</text>
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<!-- 2&#45;&gt;1 -->
<g id="edge2" class="edge">
<title>2&#45;&gt;1</title>
<path fill="none" stroke="grey" stroke-width="2" d="M99,-159.66C99,-151.7 99,-142.76 99,-134.24"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="102.5,-134.16 99,-124.16 95.5,-134.16 102.5,-134.16"/>
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<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
<path fill="none" stroke="#56d8b1" stroke-width="2" d="M154.5,-284C154.5,-284 119.5,-284 119.5,-284 113.5,-284 107.5,-278 107.5,-272 107.5,-272 107.5,-260 107.5,-260 107.5,-254 113.5,-248 119.5,-248 119.5,-248 154.5,-248 154.5,-248 160.5,-248 166.5,-254 166.5,-260 166.5,-260 166.5,-272 166.5,-272 166.5,-278 160.5,-284 154.5,-284"/>
<text text-anchor="middle" x="137" y="-263.5" font-family="sans" font-size="10.00">run RAFT</text>
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<!-- 3&#45;&gt;2 -->
<g id="edge3" class="edge">
<title>3&#45;&gt;2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M128.57,-247.69C124.8,-239.96 120.23,-230.57 115.81,-221.5"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="118.83,-219.71 111.3,-212.26 112.54,-222.78 118.83,-219.71"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
<path fill="none" stroke="#97d856" stroke-width="2" d="M238.5,-719C238.5,-719 161.5,-719 161.5,-719 155.5,-719 149.5,-713 149.5,-707 149.5,-707 149.5,-668 149.5,-668 149.5,-662 155.5,-656 161.5,-656 161.5,-656 238.5,-656 238.5,-656 244.5,-656 250.5,-662 250.5,-668 250.5,-668 250.5,-707 250.5,-707 250.5,-713 244.5,-719 238.5,-719"/>
<text text-anchor="middle" x="200" y="-707" font-family="sans" font-size="10.00">run hifiasm with</text>
<text text-anchor="middle" x="200" y="-696" font-family="sans" font-size="10.00">defaults to get</text>
<text text-anchor="middle" x="200" y="-685" font-family="sans" font-size="10.00">another 3 rounds</text>
<text text-anchor="middle" x="200" y="-674" font-family="sans" font-size="10.00">of error&#45;corrected</text>
<text text-anchor="middle" x="200" y="-663" font-family="sans" font-size="10.00">reads</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge5" class="edge">
<title>4&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M174.24,-655.73C151.52,-625.38 122,-576.68 122,-528.5 122,-528.5 122,-528.5 122,-444 122,-390.85 128.8,-329.04 133.24,-294.32"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="136.76,-294.42 134.59,-284.05 129.82,-293.51 136.76,-294.42"/>
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<!-- 38 -->
<g id="node39" class="node">
<title>38</title>
<path fill="none" stroke="#56d86b" stroke-width="2" d="M228,-620C228,-620 172,-620 172,-620 166,-620 160,-614 160,-608 160,-608 160,-596 160,-596 160,-590 166,-584 172,-584 172,-584 228,-584 228,-584 234,-584 240,-590 240,-596 240,-596 240,-608 240,-608 240,-614 234,-620 228,-620"/>
<text text-anchor="middle" x="200" y="-605" font-family="sans" font-size="10.00">run hifiasm to</text>
<text text-anchor="middle" x="200" y="-594" font-family="sans" font-size="10.00">get overlaps</text>
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<!-- 4&#45;&gt;38 -->
<g id="edge53" class="edge">
<title>4&#45;&gt;38</title>
<path fill="none" stroke="grey" stroke-width="2" d="M200,-655.88C200,-647.47 200,-638.4 200,-630.19"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="203.5,-630.03 200,-620.03 196.5,-630.03 203.5,-630.03"/>
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<!-- 40 -->
<g id="node41" class="node">
<title>40</title>
<path fill="none" stroke="#56d8c1" stroke-width="2" d="M322.5,-471C322.5,-471 253.5,-471 253.5,-471 247.5,-471 241.5,-465 241.5,-459 241.5,-459 241.5,-431 241.5,-431 241.5,-425 247.5,-419 253.5,-419 253.5,-419 322.5,-419 322.5,-419 328.5,-419 334.5,-425 334.5,-431 334.5,-431 334.5,-459 334.5,-459 334.5,-465 328.5,-471 322.5,-471"/>
<text text-anchor="middle" x="288" y="-459" font-family="sans" font-size="10.00">run mm2&#45;fast</text>
<text text-anchor="middle" x="288" y="-448" font-family="sans" font-size="10.00">to get alignment</text>
<text text-anchor="middle" x="288" y="-437" font-family="sans" font-size="10.00"> error&#45;rates to</text>
<text text-anchor="middle" x="288" y="-426" font-family="sans" font-size="10.00"> chr17</text>
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<!-- 4&#45;&gt;40 -->
<g id="edge56" class="edge">
<title>4&#45;&gt;40</title>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
<path fill="none" stroke="#56b9d8" stroke-width="2" d="M262.5,-791C262.5,-791 137.5,-791 137.5,-791 131.5,-791 125.5,-785 125.5,-779 125.5,-779 125.5,-767 125.5,-767 125.5,-761 131.5,-755 137.5,-755 137.5,-755 262.5,-755 262.5,-755 268.5,-755 274.5,-761 274.5,-767 274.5,-767 274.5,-779 274.5,-779 274.5,-785 268.5,-791 262.5,-791"/>
<text text-anchor="middle" x="200" y="-770.5" font-family="sans" font-size="10.00">compress 3x corrected reads</text>
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<!-- 5&#45;&gt;4 -->
<g id="edge8" class="edge">
<title>5&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M200,-754.7C200,-747.27 200,-738.25 200,-729.29"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="203.5,-729.28 200,-719.28 196.5,-729.28 203.5,-729.28"/>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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<text text-anchor="middle" x="200" y="-848" font-family="sans" font-size="10.00">error&#45;correct the</text>
<text text-anchor="middle" x="200" y="-837" font-family="sans" font-size="10.00">2x corrected reads</text>
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<!-- 6&#45;&gt;5 -->
<g id="edge9" class="edge">
<title>6&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M200,-826.7C200,-818.98 200,-809.71 200,-801.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="203.5,-801.1 200,-791.1 196.5,-801.1 203.5,-801.1"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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<text text-anchor="middle" x="173" y="-1072" font-family="sans" font-size="10.00">make a sequence</text>
<text text-anchor="middle" x="173" y="-1061" font-family="sans" font-size="10.00">database for the</text>
<text text-anchor="middle" x="173" y="-1050" font-family="sans" font-size="10.00">2x corrected HiFi reads</text>
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<!-- 7&#45;&gt;6 -->
<g id="edge11" class="edge">
<title>7&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M165.07,-1042.92C153.57,-1011.51 135.56,-948.39 154,-899 157.88,-888.62 164.8,-878.93 172.12,-870.74"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="174.78,-873.03 179.18,-863.38 169.73,-868.18 174.78,-873.03"/>
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<!-- 36 -->
<g id="node37" class="node">
<title>36</title>
<path fill="none" stroke="#afd856" stroke-width="2" d="M240.5,-935C240.5,-935 175.5,-935 175.5,-935 169.5,-935 163.5,-929 163.5,-923 163.5,-923 163.5,-911 163.5,-911 163.5,-905 169.5,-899 175.5,-899 175.5,-899 240.5,-899 240.5,-899 246.5,-899 252.5,-905 252.5,-911 252.5,-911 252.5,-923 252.5,-923 252.5,-929 246.5,-935 240.5,-935"/>
<text text-anchor="middle" x="208" y="-920" font-family="sans" font-size="10.00">overlap the 2x</text>
<text text-anchor="middle" x="208" y="-909" font-family="sans" font-size="10.00">corrected reads</text>
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<!-- 7&#45;&gt;36 -->
<g id="edge51" class="edge">
<title>7&#45;&gt;36</title>
<path fill="none" stroke="grey" stroke-width="2" d="M176.58,-1042.75C180.07,-1024.14 185.76,-995.53 192,-971 194.19,-962.39 196.88,-953.09 199.43,-944.72"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="202.8,-945.67 202.42,-935.08 196.12,-943.59 202.8,-945.67"/>
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<!-- 37 -->
<g id="node38" class="node">
<title>37</title>
<path fill="none" stroke="#d86e56" stroke-width="2" d="M326.5,-1007C326.5,-1007 213.5,-1007 213.5,-1007 207.5,-1007 201.5,-1001 201.5,-995 201.5,-995 201.5,-983 201.5,-983 201.5,-977 207.5,-971 213.5,-971 213.5,-971 326.5,-971 326.5,-971 332.5,-971 338.5,-977 338.5,-983 338.5,-983 338.5,-995 338.5,-995 338.5,-1001 332.5,-1007 326.5,-1007"/>
<text text-anchor="middle" x="270" y="-992" font-family="sans" font-size="10.00">make a shimmer index</text>
<text text-anchor="middle" x="270" y="-981" font-family="sans" font-size="10.00">for the 2x corrected reads</text>
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<!-- 7&#45;&gt;37 -->
<g id="edge52" class="edge">
<title>7&#45;&gt;37</title>
<path fill="none" stroke="grey" stroke-width="2" d="M199.25,-1042.88C211.49,-1033.73 226.15,-1022.77 238.94,-1013.21"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="241.12,-1015.96 247.03,-1007.17 236.93,-1010.35 241.12,-1015.96"/>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
<path fill="none" stroke="#5692d8" stroke-width="2" d="M226.5,-1161C226.5,-1161 119.5,-1161 119.5,-1161 113.5,-1161 107.5,-1155 107.5,-1149 107.5,-1149 107.5,-1132 107.5,-1132 107.5,-1126 113.5,-1120 119.5,-1120 119.5,-1120 226.5,-1120 226.5,-1120 232.5,-1120 238.5,-1126 238.5,-1132 238.5,-1132 238.5,-1149 238.5,-1149 238.5,-1155 232.5,-1161 226.5,-1161"/>
<text text-anchor="middle" x="173" y="-1149" font-family="sans" font-size="10.00">make a file listing</text>
<text text-anchor="middle" x="173" y="-1138" font-family="sans" font-size="10.00">the locations of the</text>
<text text-anchor="middle" x="173" y="-1127" font-family="sans" font-size="10.00">2x error&#45;corrected reads</text>
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<!-- 8&#45;&gt;7 -->
<g id="edge12" class="edge">
<title>8&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M173,-1119.79C173,-1111.96 173,-1102.77 173,-1094.16"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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<text text-anchor="middle" x="172" y="-1284.5" font-family="sans" font-size="10.00">compress 2x corrected reads</text>
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<!-- 9&#45;&gt;8 -->
<g id="edge14" class="edge">
<title>9&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M172.12,-1268.86C172.28,-1244.89 172.59,-1200.99 172.79,-1171.53"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="176.29,-1171.42 172.86,-1161.39 169.29,-1171.37 176.29,-1171.42"/>
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<!-- 35 -->
<g id="node36" class="node">
<title>35</title>
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<text text-anchor="middle" x="243" y="-1218" font-family="sans" font-size="10.00">compress 2nd</text>
<text text-anchor="middle" x="243" y="-1207" font-family="sans" font-size="10.00">set of overlaps</text>
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<!-- 9&#45;&gt;35 -->
<g id="edge49" class="edge">
<title>9&#45;&gt;35</title>
<path fill="none" stroke="grey" stroke-width="2" d="M189.55,-1268.7C198.23,-1260.14 208.86,-1249.66 218.35,-1240.3"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
<path fill="none" stroke="#566bd8" stroke-width="2" d="M211.5,-1377C211.5,-1377 132.5,-1377 132.5,-1377 126.5,-1377 120.5,-1371 120.5,-1365 120.5,-1365 120.5,-1353 120.5,-1353 120.5,-1347 126.5,-1341 132.5,-1341 132.5,-1341 211.5,-1341 211.5,-1341 217.5,-1341 223.5,-1347 223.5,-1353 223.5,-1353 223.5,-1365 223.5,-1365 223.5,-1371 217.5,-1377 211.5,-1377"/>
<text text-anchor="middle" x="172" y="-1362" font-family="sans" font-size="10.00">error&#45;correct the</text>
<text text-anchor="middle" x="172" y="-1351" font-family="sans" font-size="10.00">1x corrected reads</text>
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<!-- 10&#45;&gt;9 -->
<g id="edge15" class="edge">
<title>10&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M172,-1340.7C172,-1332.98 172,-1323.71 172,-1315.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="175.5,-1315.1 172,-1305.1 168.5,-1315.1 175.5,-1315.1"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
<path fill="none" stroke="#d8d356" stroke-width="2" d="M233.5,-1593C233.5,-1593 116.5,-1593 116.5,-1593 110.5,-1593 104.5,-1587 104.5,-1581 104.5,-1581 104.5,-1569 104.5,-1569 104.5,-1563 110.5,-1557 116.5,-1557 116.5,-1557 233.5,-1557 233.5,-1557 239.5,-1557 245.5,-1563 245.5,-1569 245.5,-1569 245.5,-1581 245.5,-1581 245.5,-1587 239.5,-1593 233.5,-1593"/>
<text text-anchor="middle" x="175" y="-1578" font-family="sans" font-size="10.00">make a sequence database</text>
<text text-anchor="middle" x="175" y="-1567" font-family="sans" font-size="10.00">for the 1x corrected reads</text>
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<!-- 11&#45;&gt;10 -->
<g id="edge17" class="edge">
<title>11&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M174.76,-1556.85C174.24,-1519.83 173.01,-1432.18 172.38,-1387.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="175.88,-1387.18 172.24,-1377.23 168.88,-1387.28 175.88,-1387.18"/>
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<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
<path fill="none" stroke="#56d0d8" stroke-width="2" d="M273.5,-1449C273.5,-1449 208.5,-1449 208.5,-1449 202.5,-1449 196.5,-1443 196.5,-1437 196.5,-1437 196.5,-1425 196.5,-1425 196.5,-1419 202.5,-1413 208.5,-1413 208.5,-1413 273.5,-1413 273.5,-1413 279.5,-1413 285.5,-1419 285.5,-1425 285.5,-1425 285.5,-1437 285.5,-1437 285.5,-1443 279.5,-1449 273.5,-1449"/>
<text text-anchor="middle" x="241" y="-1434" font-family="sans" font-size="10.00">overlap the 1x</text>
<text text-anchor="middle" x="241" y="-1423" font-family="sans" font-size="10.00">corrected reads</text>
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<!-- 11&#45;&gt;33 -->
<g id="edge45" class="edge">
<title>11&#45;&gt;33</title>
<path fill="none" stroke="grey" stroke-width="2" d="M176.07,-1556.74C177.8,-1538.15 182.31,-1508.13 194,-1485 199.18,-1474.75 206.84,-1464.92 214.47,-1456.57"/>
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<!-- 34 -->
<g id="node35" class="node">
<title>34</title>
<path fill="none" stroke="#56d8c9" stroke-width="2" d="M328.5,-1521C328.5,-1521 215.5,-1521 215.5,-1521 209.5,-1521 203.5,-1515 203.5,-1509 203.5,-1509 203.5,-1497 203.5,-1497 203.5,-1491 209.5,-1485 215.5,-1485 215.5,-1485 328.5,-1485 328.5,-1485 334.5,-1485 340.5,-1491 340.5,-1497 340.5,-1497 340.5,-1509 340.5,-1509 340.5,-1515 334.5,-1521 328.5,-1521"/>
<text text-anchor="middle" x="272" y="-1506" font-family="sans" font-size="10.00">make a shimmer index</text>
<text text-anchor="middle" x="272" y="-1495" font-family="sans" font-size="10.00">for the 1x corrected reads</text>
</g>
<!-- 11&#45;&gt;34 -->
<g id="edge47" class="edge">
<title>11&#45;&gt;34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M198.98,-1556.7C211.31,-1547.8 226.52,-1536.82 239.85,-1527.2"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="242.24,-1529.79 248.3,-1521.1 238.14,-1524.12 242.24,-1529.79"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
<path fill="none" stroke="#567bd8" stroke-width="2" d="M230.5,-1670C230.5,-1670 119.5,-1670 119.5,-1670 113.5,-1670 107.5,-1664 107.5,-1658 107.5,-1658 107.5,-1641 107.5,-1641 107.5,-1635 113.5,-1629 119.5,-1629 119.5,-1629 230.5,-1629 230.5,-1629 236.5,-1629 242.5,-1635 242.5,-1641 242.5,-1641 242.5,-1658 242.5,-1658 242.5,-1664 236.5,-1670 230.5,-1670"/>
<text text-anchor="middle" x="175" y="-1658" font-family="sans" font-size="10.00">make a file listing</text>
<text text-anchor="middle" x="175" y="-1647" font-family="sans" font-size="10.00">the locations of</text>
<text text-anchor="middle" x="175" y="-1636" font-family="sans" font-size="10.00">the error&#45;corrected reads</text>
</g>
<!-- 12&#45;&gt;11 -->
<g id="edge18" class="edge">
<title>12&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M175,-1628.69C175,-1620.91 175,-1611.84 175,-1603.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="178.5,-1603.32 175,-1593.32 171.5,-1603.32 178.5,-1603.32"/>
</g>
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
<path fill="none" stroke="#d85656" stroke-width="2" d="M177.5,-1742C177.5,-1742 112.5,-1742 112.5,-1742 106.5,-1742 100.5,-1736 100.5,-1730 100.5,-1730 100.5,-1718 100.5,-1718 100.5,-1712 106.5,-1706 112.5,-1706 112.5,-1706 177.5,-1706 177.5,-1706 183.5,-1706 189.5,-1712 189.5,-1718 189.5,-1718 189.5,-1730 189.5,-1730 189.5,-1736 183.5,-1742 177.5,-1742"/>
<text text-anchor="middle" x="145" y="-1727" font-family="sans" font-size="10.00">compress 1x</text>
<text text-anchor="middle" x="145" y="-1716" font-family="sans" font-size="10.00">corrected reads</text>
</g>
<!-- 13&#45;&gt;12 -->
<g id="edge19" class="edge">
<title>13&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M152.11,-1705.82C155.37,-1697.95 159.32,-1688.4 163.02,-1679.46"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="166.29,-1680.7 166.88,-1670.12 159.82,-1678.02 166.29,-1680.7"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
<path fill="none" stroke="#d89c56" stroke-width="2" d="M209.5,-1814C209.5,-1814 110.5,-1814 110.5,-1814 104.5,-1814 98.5,-1808 98.5,-1802 98.5,-1802 98.5,-1790 98.5,-1790 98.5,-1784 104.5,-1778 110.5,-1778 110.5,-1778 209.5,-1778 209.5,-1778 215.5,-1778 221.5,-1784 221.5,-1790 221.5,-1790 221.5,-1802 221.5,-1802 221.5,-1808 215.5,-1814 209.5,-1814"/>
<text text-anchor="middle" x="160" y="-1793.5" font-family="sans" font-size="10.00">error&#45;correct the reads</text>
</g>
<!-- 14&#45;&gt;13 -->
<g id="edge21" class="edge">
<title>14&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M156.29,-1777.7C154.64,-1769.98 152.65,-1760.71 150.81,-1752.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="154.18,-1751.15 148.67,-1742.1 147.34,-1752.62 154.18,-1751.15"/>
</g>
<!-- 32 -->
<g id="node33" class="node">
<title>32</title>
<path fill="none" stroke="#d86656" stroke-width="2" d="M280.5,-1742C280.5,-1742 219.5,-1742 219.5,-1742 213.5,-1742 207.5,-1736 207.5,-1730 207.5,-1730 207.5,-1718 207.5,-1718 207.5,-1712 213.5,-1706 219.5,-1706 219.5,-1706 280.5,-1706 280.5,-1706 286.5,-1706 292.5,-1712 292.5,-1718 292.5,-1718 292.5,-1730 292.5,-1730 292.5,-1736 286.5,-1742 280.5,-1742"/>
<text text-anchor="middle" x="250" y="-1727" font-family="sans" font-size="10.00">compress 1st</text>
<text text-anchor="middle" x="250" y="-1716" font-family="sans" font-size="10.00">set of overlaps</text>
</g>
<!-- 14&#45;&gt;32 -->
<g id="edge44" class="edge">
<title>14&#45;&gt;32</title>
<path fill="none" stroke="grey" stroke-width="2" d="M182.25,-1777.7C193.58,-1768.88 207.53,-1758.03 219.82,-1748.47"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="222.26,-1751.01 228.01,-1742.1 217.97,-1745.48 222.26,-1751.01"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
<path fill="none" stroke="#d8c356" stroke-width="2" d="M241.5,-2030C241.5,-2030 144.5,-2030 144.5,-2030 138.5,-2030 132.5,-2024 132.5,-2018 132.5,-2018 132.5,-2006 132.5,-2006 132.5,-2000 138.5,-1994 144.5,-1994 144.5,-1994 241.5,-1994 241.5,-1994 247.5,-1994 253.5,-2000 253.5,-2006 253.5,-2006 253.5,-2018 253.5,-2018 253.5,-2024 247.5,-2030 241.5,-2030"/>
<text text-anchor="middle" x="193" y="-2015" font-family="sans" font-size="10.00">make a sequence</text>
<text text-anchor="middle" x="193" y="-2004" font-family="sans" font-size="10.00">database for the reads</text>
</g>
<!-- 15&#45;&gt;14 -->
<g id="edge23" class="edge">
<title>15&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M190.36,-1993.85C184.65,-1956.83 171.13,-1869.18 164.22,-1824.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="167.64,-1823.58 162.66,-1814.23 160.72,-1824.65 167.64,-1823.58"/>
</g>
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
<path fill="none" stroke="#56d882" stroke-width="2" d="M278,-1886C278,-1886 204,-1886 204,-1886 198,-1886 192,-1880 192,-1874 192,-1874 192,-1862 192,-1862 192,-1856 198,-1850 204,-1850 204,-1850 278,-1850 278,-1850 284,-1850 290,-1856 290,-1862 290,-1862 290,-1874 290,-1874 290,-1880 284,-1886 278,-1886"/>
<text text-anchor="middle" x="241" y="-1865.5" font-family="sans" font-size="10.00">overlap the reads</text>
</g>
<!-- 15&#45;&gt;30 -->
<g id="edge41" class="edge">
<title>15&#45;&gt;30</title>
<path fill="none" stroke="grey" stroke-width="2" d="M195.15,-1993.86C197.78,-1975.62 203.04,-1946.14 212,-1922 215.4,-1912.86 220.15,-1903.36 224.83,-1894.98"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="228.01,-1896.47 230,-1886.06 221.96,-1892.95 228.01,-1896.47"/>
</g>
<!-- 31 -->
<g id="node32" class="node">
<title>31</title>
<path fill="none" stroke="#d88556" stroke-width="2" d="M329,-1958C329,-1958 233,-1958 233,-1958 227,-1958 221,-1952 221,-1946 221,-1946 221,-1934 221,-1934 221,-1928 227,-1922 233,-1922 233,-1922 329,-1922 329,-1922 335,-1922 341,-1928 341,-1934 341,-1934 341,-1946 341,-1946 341,-1952 335,-1958 329,-1958"/>
<text text-anchor="middle" x="281" y="-1943" font-family="sans" font-size="10.00">make a shimmer index</text>
<text text-anchor="middle" x="281" y="-1932" font-family="sans" font-size="10.00">for the reads</text>
</g>
<!-- 15&#45;&gt;31 -->
<g id="edge42" class="edge">
<title>15&#45;&gt;31</title>
<path fill="none" stroke="grey" stroke-width="2" d="M214.75,-1993.7C225.84,-1984.88 239.47,-1974.03 251.49,-1964.47"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="253.85,-1967.07 259.5,-1958.1 249.49,-1961.59 253.85,-1967.07"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
<path fill="none" stroke="#568ad8" stroke-width="2" d="M264.5,-2118C264.5,-2118 121.5,-2118 121.5,-2118 115.5,-2118 109.5,-2112 109.5,-2106 109.5,-2106 109.5,-2078 109.5,-2078 109.5,-2072 115.5,-2066 121.5,-2066 121.5,-2066 264.5,-2066 264.5,-2066 270.5,-2066 276.5,-2072 276.5,-2078 276.5,-2078 276.5,-2106 276.5,-2106 276.5,-2112 270.5,-2118 264.5,-2118"/>
<text text-anchor="middle" x="193" y="-2106" font-family="sans" font-size="10.00">make a file listing</text>
<text text-anchor="middle" x="193" y="-2095" font-family="sans" font-size="10.00">the location of the</text>
<text text-anchor="middle" x="193" y="-2084" font-family="sans" font-size="10.00">racon/brutal_rewrite/kmer_filter</text>
<text text-anchor="middle" x="193" y="-2073" font-family="sans" font-size="10.00">corrected reads</text>
</g>
<!-- 16&#45;&gt;15 -->
<g id="edge24" class="edge">
<title>16&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2065.89C193,-2057.84 193,-2048.88 193,-2040.66"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2040.41 193,-2030.41 189.5,-2040.41 196.5,-2040.41"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
<path fill="none" stroke="#56a9d8" stroke-width="2" d="M225.5,-2206C225.5,-2206 160.5,-2206 160.5,-2206 154.5,-2206 148.5,-2200 148.5,-2194 148.5,-2194 148.5,-2166 148.5,-2166 148.5,-2160 154.5,-2154 160.5,-2154 160.5,-2154 225.5,-2154 225.5,-2154 231.5,-2154 237.5,-2160 237.5,-2166 237.5,-2166 237.5,-2194 237.5,-2194 237.5,-2200 231.5,-2206 225.5,-2206"/>
<text text-anchor="middle" x="193" y="-2194" font-family="sans" font-size="10.00">put all 8</text>
<text text-anchor="middle" x="193" y="-2183" font-family="sans" font-size="10.00">files of</text>
<text text-anchor="middle" x="193" y="-2172" font-family="sans" font-size="10.00">shredded reads</text>
<text text-anchor="middle" x="193" y="-2161" font-family="sans" font-size="10.00">back together</text>
</g>
<!-- 17&#45;&gt;16 -->
<g id="edge25" class="edge">
<title>17&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2153.66C193,-2145.7 193,-2136.76 193,-2128.24"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2128.16 193,-2118.16 189.5,-2128.16 196.5,-2128.16"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
<path fill="none" stroke="#56d8a2" stroke-width="2" d="M216.5,-2283C216.5,-2283 169.5,-2283 169.5,-2283 163.5,-2283 157.5,-2277 157.5,-2271 157.5,-2271 157.5,-2254 157.5,-2254 157.5,-2248 163.5,-2242 169.5,-2242 169.5,-2242 216.5,-2242 216.5,-2242 222.5,-2242 228.5,-2248 228.5,-2254 228.5,-2254 228.5,-2271 228.5,-2271 228.5,-2277 222.5,-2283 216.5,-2283"/>
<text text-anchor="middle" x="193" y="-2271" font-family="sans" font-size="10.00">shred reads</text>
<text text-anchor="middle" x="193" y="-2260" font-family="sans" font-size="10.00">into pieces</text>
<text text-anchor="middle" x="193" y="-2249" font-family="sans" font-size="10.00">&lt;90 Kbp</text>
</g>
<!-- 18&#45;&gt;17 -->
<g id="edge26" class="edge">
<title>18&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2241.6C193,-2233.99 193,-2225.06 193,-2216.43"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2216.16 193,-2206.16 189.5,-2216.16 196.5,-2216.16"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
<path fill="none" stroke="#5663d8" stroke-width="2" d="M221,-2360C221,-2360 165,-2360 165,-2360 159,-2360 153,-2354 153,-2348 153,-2348 153,-2331 153,-2331 153,-2325 159,-2319 165,-2319 165,-2319 221,-2319 221,-2319 227,-2319 233,-2325 233,-2331 233,-2331 233,-2348 233,-2348 233,-2354 227,-2360 221,-2360"/>
<text text-anchor="middle" x="193" y="-2348" font-family="sans" font-size="10.00">split reads</text>
<text text-anchor="middle" x="193" y="-2337" font-family="sans" font-size="10.00">into 8 files</text>
<text text-anchor="middle" x="193" y="-2326" font-family="sans" font-size="10.00">for shredding</text>
</g>
<!-- 19&#45;&gt;18 -->
<g id="edge27" class="edge">
<title>19&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2318.79C193,-2310.96 193,-2301.77 193,-2293.16"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2293.07 193,-2283.07 189.5,-2293.07 196.5,-2293.07"/>
</g>
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
<path fill="none" stroke="#56a2d8" stroke-width="2" d="M226,-2437C226,-2437 160,-2437 160,-2437 154,-2437 148,-2431 148,-2425 148,-2425 148,-2408 148,-2408 148,-2402 154,-2396 160,-2396 160,-2396 226,-2396 226,-2396 232,-2396 238,-2402 238,-2408 238,-2408 238,-2425 238,-2425 238,-2431 232,-2437 226,-2437"/>
<text text-anchor="middle" x="193" y="-2425" font-family="sans" font-size="10.00">k&#45;mer filtering </text>
<text text-anchor="middle" x="193" y="-2414" font-family="sans" font-size="10.00">of bad reads </text>
<text text-anchor="middle" x="193" y="-2403" font-family="sans" font-size="10.00">with kmer_filter</text>
</g>
<!-- 20&#45;&gt;19 -->
<g id="edge28" class="edge">
<title>20&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2395.79C193,-2387.96 193,-2378.77 193,-2370.16"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2370.07 193,-2360.07 189.5,-2370.07 196.5,-2370.07"/>
</g>
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
<path fill="none" stroke="#bed856" stroke-width="2" d="M242,-2509C242,-2509 144,-2509 144,-2509 138,-2509 132,-2503 132,-2497 132,-2497 132,-2485 132,-2485 132,-2479 138,-2473 144,-2473 144,-2473 242,-2473 242,-2473 248,-2473 254,-2479 254,-2485 254,-2485 254,-2497 254,-2497 254,-2503 248,-2509 242,-2509"/>
<text text-anchor="middle" x="193" y="-2494" font-family="sans" font-size="10.00">k&#45;mer error&#45;correction</text>
<text text-anchor="middle" x="193" y="-2483" font-family="sans" font-size="10.00">with brutal rewrite</text>
</g>
<!-- 21&#45;&gt;20 -->
<g id="edge29" class="edge">
<title>21&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2472.82C193,-2465.2 193,-2456 193,-2447.32"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2447.12 193,-2437.12 189.5,-2447.12 196.5,-2447.12"/>
</g>
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
<path fill="none" stroke="#d87d56" stroke-width="2" d="M239,-2586C239,-2586 147,-2586 147,-2586 141,-2586 135,-2580 135,-2574 135,-2574 135,-2557 135,-2557 135,-2551 141,-2545 147,-2545 147,-2545 239,-2545 239,-2545 245,-2545 251,-2551 251,-2557 251,-2557 251,-2574 251,-2574 251,-2580 245,-2586 239,-2586"/>
<text text-anchor="middle" x="193" y="-2574" font-family="sans" font-size="10.00">error&#45;correct reads</text>
<text text-anchor="middle" x="193" y="-2563" font-family="sans" font-size="10.00">with overlap info with</text>
<text text-anchor="middle" x="193" y="-2552" font-family="sans" font-size="10.00">racon from vechat</text>
</g>
<!-- 22&#45;&gt;21 -->
<g id="edge30" class="edge">
<title>22&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M193,-2544.69C193,-2536.91 193,-2527.84 193,-2519.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="196.5,-2519.32 193,-2509.32 189.5,-2519.32 196.5,-2519.32"/>
</g>
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
<path fill="none" stroke="#c6d856" stroke-width="2" d="M180,-2746C180,-2746 124,-2746 124,-2746 118,-2746 112,-2740 112,-2734 112,-2734 112,-2722 112,-2722 112,-2716 118,-2710 124,-2710 124,-2710 180,-2710 180,-2710 186,-2710 192,-2716 192,-2722 192,-2722 192,-2734 192,-2734 192,-2740 186,-2746 180,-2746"/>
<text text-anchor="middle" x="152" y="-2731" font-family="sans" font-size="10.00">convert bam</text>
<text text-anchor="middle" x="152" y="-2720" font-family="sans" font-size="10.00">files to FASTQ</text>
</g>
<!-- 23&#45;&gt;2 -->
<g id="edge4" class="edge">
<title>23&#45;&gt;2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M136.19,-2709.72C112.36,-2681.8 70,-2624.07 70,-2566.5 70,-2566.5 70,-2566.5 70,-350.5 70,-305.76 80.66,-255.17 89.05,-222.27"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="92.53,-222.8 91.68,-212.24 85.76,-221.03 92.53,-222.8"/>
</g>
<!-- 23&#45;&gt;22 -->
<g id="edge32" class="edge">
<title>23&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M141.89,-2709.94C130.64,-2688.56 115.67,-2651.2 129,-2622 134.15,-2610.71 142.86,-2600.83 152.22,-2592.67"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="154.61,-2595.23 160.17,-2586.21 150.2,-2589.8 154.61,-2595.23"/>
</g>
<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
<path fill="none" stroke="#d6d856" stroke-width="2" d="M239.5,-2674C239.5,-2674 150.5,-2674 150.5,-2674 144.5,-2674 138.5,-2668 138.5,-2662 138.5,-2662 138.5,-2634 138.5,-2634 138.5,-2628 144.5,-2622 150.5,-2622 150.5,-2622 239.5,-2622 239.5,-2622 245.5,-2622 251.5,-2628 251.5,-2634 251.5,-2634 251.5,-2662 251.5,-2662 251.5,-2668 245.5,-2674 239.5,-2674"/>
<text text-anchor="middle" x="195" y="-2662" font-family="sans" font-size="10.00">use mm2&#45;fast</text>
<text text-anchor="middle" x="195" y="-2651" font-family="sans" font-size="10.00">to overlap SUP reads</text>
<text text-anchor="middle" x="195" y="-2640" font-family="sans" font-size="10.00">and filter overlaps</text>
<text text-anchor="middle" x="195" y="-2629" font-family="sans" font-size="10.00">with awk and fpa</text>
</g>
<!-- 23&#45;&gt;29 -->
<g id="edge39" class="edge">
<title>23&#45;&gt;29</title>
<path fill="none" stroke="grey" stroke-width="2" d="M161.54,-2709.69C165.85,-2701.88 171.09,-2692.37 176.14,-2683.22"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="179.31,-2684.7 181.08,-2674.26 173.18,-2681.32 179.31,-2684.7"/>
</g>
<!-- 23&#45;&gt;40 -->
<g id="edge57" class="edge">
<title>23&#45;&gt;40</title>
<path fill="none" stroke="grey" stroke-width="2" d="M192.05,-2717.04C254.75,-2698.77 369,-2653.54 369,-2566.5 369,-2566.5 369,-2566.5 369,-601 369,-554.79 340.37,-508.74 317.16,-479"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="319.77,-476.66 310.78,-471.05 314.31,-481.04 319.77,-476.66"/>
</g>
<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
<path fill="none" stroke="#78d856" stroke-width="2" d="M128,-2818C128,-2818 12,-2818 12,-2818 6,-2818 0,-2812 0,-2806 0,-2806 0,-2794 0,-2794 0,-2788 6,-2782 12,-2782 12,-2782 128,-2782 128,-2782 134,-2782 140,-2788 140,-2794 140,-2794 140,-2806 140,-2806 140,-2812 134,-2818 128,-2818"/>
<text text-anchor="middle" x="70" y="-2803" font-family="sans" font-size="10.00">use dorado to basecall</text>
<text text-anchor="middle" x="70" y="-2792" font-family="sans" font-size="10.00">squiggles using SUP model</text>
</g>
<!-- 24&#45;&gt;23 -->
<g id="edge33" class="edge">
<title>24&#45;&gt;23</title>
<path fill="none" stroke="grey" stroke-width="2" d="M90.27,-2781.7C100.5,-2772.97 113.06,-2762.24 124.18,-2752.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="126.63,-2755.26 131.96,-2746.1 122.09,-2749.94 126.63,-2755.26"/>
</g>
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
<path fill="none" stroke="#a7d856" stroke-width="2" d="M234,-2890C234,-2890 70,-2890 70,-2890 64,-2890 58,-2884 58,-2878 58,-2878 58,-2866 58,-2866 58,-2860 64,-2854 70,-2854 70,-2854 234,-2854 234,-2854 240,-2854 246,-2860 246,-2866 246,-2866 246,-2878 246,-2878 246,-2884 240,-2890 234,-2890"/>
<text text-anchor="middle" x="152" y="-2875" font-family="sans" font-size="10.00">use blue_crab to convert</text>
<text text-anchor="middle" x="152" y="-2864" font-family="sans" font-size="10.00">squiggles from blow5 to pod5 format</text>
</g>
<!-- 25&#45;&gt;24 -->
<g id="edge35" class="edge">
<title>25&#45;&gt;24</title>
<path fill="none" stroke="grey" stroke-width="2" d="M131.73,-2853.7C121.5,-2844.97 108.94,-2834.24 97.82,-2824.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="99.91,-2821.94 90.04,-2818.1 95.37,-2827.26 99.91,-2821.94"/>
</g>
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
<path fill="none" stroke="#68d856" stroke-width="2" d="M298,-2818C298,-2818 170,-2818 170,-2818 164,-2818 158,-2812 158,-2806 158,-2806 158,-2794 158,-2794 158,-2788 164,-2782 170,-2782 170,-2782 298,-2782 298,-2782 304,-2782 310,-2788 310,-2794 310,-2794 310,-2806 310,-2806 310,-2812 304,-2818 298,-2818"/>
<text text-anchor="middle" x="234" y="-2803" font-family="sans" font-size="10.00">use dorado to basecall</text>
<text text-anchor="middle" x="234" y="-2792" font-family="sans" font-size="10.00">squiggles using duplex model</text>
</g>
<!-- 25&#45;&gt;28 -->
<g id="edge38" class="edge">
<title>25&#45;&gt;28</title>
<path fill="none" stroke="grey" stroke-width="2" d="M172.27,-2853.7C182.5,-2844.97 195.06,-2834.24 206.18,-2824.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="208.63,-2827.26 213.96,-2818.1 204.09,-2821.94 208.63,-2827.26"/>
</g>
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
<path fill="none" stroke="#d8ac56" stroke-width="2" d="M205,-2967C205,-2967 99,-2967 99,-2967 93,-2967 87,-2961 87,-2955 87,-2955 87,-2938 87,-2938 87,-2932 93,-2926 99,-2926 99,-2926 205,-2926 205,-2926 211,-2926 217,-2932 217,-2938 217,-2938 217,-2955 217,-2955 217,-2961 211,-2967 205,-2967"/>
<text text-anchor="middle" x="152" y="-2955" font-family="sans" font-size="10.00">use slow5tools to extract</text>
<text text-anchor="middle" x="152" y="-2944" font-family="sans" font-size="10.00">squiggles for desired</text>
<text text-anchor="middle" x="152" y="-2933" font-family="sans" font-size="10.00">chr17 reads</text>
</g>
<!-- 26&#45;&gt;25 -->
<g id="edge36" class="edge">
<title>26&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M152,-2925.69C152,-2917.91 152,-2908.84 152,-2900.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="155.5,-2900.32 152,-2890.32 148.5,-2900.32 155.5,-2900.32"/>
</g>
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
<path fill="none" stroke="#56c1d8" stroke-width="2" d="M211,-3066C211,-3066 93,-3066 93,-3066 87,-3066 81,-3060 81,-3054 81,-3054 81,-3015 81,-3015 81,-3009 87,-3003 93,-3003 93,-3003 211,-3003 211,-3003 217,-3003 223,-3009 223,-3015 223,-3015 223,-3054 223,-3054 223,-3060 217,-3066 211,-3066"/>
<text text-anchor="middle" x="152" y="-3054" font-family="sans" font-size="10.00">filter gaf file for</text>
<text text-anchor="middle" x="152" y="-3043" font-family="sans" font-size="10.00">desired chromosome reads</text>
<text text-anchor="middle" x="152" y="-3032" font-family="sans" font-size="10.00">in this</text>
<text text-anchor="middle" x="152" y="-3021" font-family="sans" font-size="10.00">example:</text>
<text text-anchor="middle" x="152" y="-3010" font-family="sans" font-size="10.00">chr17</text>
</g>
<!-- 27&#45;&gt;26 -->
<g id="edge37" class="edge">
<title>27&#45;&gt;26</title>
<path fill="none" stroke="grey" stroke-width="2" d="M152,-3002.94C152,-2994.59 152,-2985.55 152,-2977.25"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="155.5,-2977.23 152,-2967.23 148.5,-2977.23 155.5,-2977.23"/>
</g>
<!-- 28&#45;&gt;23 -->
<g id="edge34" class="edge">
<title>28&#45;&gt;23</title>
<path fill="none" stroke="grey" stroke-width="2" d="M213.73,-2781.7C203.5,-2772.97 190.94,-2762.24 179.82,-2752.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="181.91,-2749.94 172.04,-2746.1 177.37,-2755.26 181.91,-2749.94"/>
</g>
<!-- 29&#45;&gt;22 -->
<g id="edge31" class="edge">
<title>29&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M194.38,-2621.97C194.18,-2613.86 193.95,-2604.78 193.74,-2596.35"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="197.24,-2596.06 193.49,-2586.15 190.24,-2596.23 197.24,-2596.06"/>
</g>
<!-- 30&#45;&gt;14 -->
<g id="edge22" class="edge">
<title>30&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M220.98,-1849.7C210.87,-1840.97 198.46,-1830.24 187.48,-1820.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="189.65,-1817.99 179.79,-1814.1 185.07,-1823.29 189.65,-1817.99"/>
</g>
<!-- 30&#45;&gt;32 -->
<g id="edge43" class="edge">
<title>30&#45;&gt;32</title>
<path fill="none" stroke="grey" stroke-width="2" d="M242.09,-1849.87C243.62,-1825.67 246.44,-1781.21 248.26,-1752.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="251.77,-1752.39 248.91,-1742.19 244.78,-1751.95 251.77,-1752.39"/>
</g>
<!-- 31&#45;&gt;30 -->
<g id="edge40" class="edge">
<title>31&#45;&gt;30</title>
<path fill="none" stroke="grey" stroke-width="2" d="M271.11,-1921.7C266.51,-1913.64 260.94,-1903.89 255.85,-1894.98"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="258.77,-1893.05 250.77,-1886.1 252.7,-1896.52 258.77,-1893.05"/>
</g>
<!-- 32&#45;&gt;12 -->
<g id="edge20" class="edge">
<title>32&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M232.23,-1705.82C223.39,-1697.28 212.51,-1686.76 202.62,-1677.2"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="204.92,-1674.55 195.3,-1670.12 200.05,-1679.59 204.92,-1674.55"/>
</g>
<!-- 33&#45;&gt;10 -->
<g id="edge16" class="edge">
<title>33&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M223.94,-1412.7C215.5,-1404.14 205.18,-1393.66 195.96,-1384.3"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="198.37,-1381.77 188.86,-1377.1 193.39,-1386.68 198.37,-1381.77"/>
</g>
<!-- 33&#45;&gt;35 -->
<g id="edge48" class="edge">
<title>33&#45;&gt;35</title>
<path fill="none" stroke="grey" stroke-width="2" d="M244.77,-1412.58C250.67,-1383.01 260.83,-1321.14 255,-1269 254.04,-1260.43 252.24,-1251.22 250.31,-1242.93"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="253.66,-1241.89 247.87,-1233.02 246.87,-1243.57 253.66,-1241.89"/>
</g>
<!-- 34&#45;&gt;33 -->
<g id="edge46" class="edge">
<title>34&#45;&gt;33</title>
<path fill="none" stroke="grey" stroke-width="2" d="M264.34,-1484.7C260.81,-1476.73 256.54,-1467.1 252.63,-1458.26"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="255.82,-1456.83 248.57,-1449.1 249.42,-1459.67 255.82,-1456.83"/>
</g>
<!-- 35&#45;&gt;8 -->
<g id="edge13" class="edge">
<title>35&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M226.41,-1196.82C218.24,-1188.36 208.21,-1177.97 199.05,-1168.48"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="201.41,-1165.88 191.94,-1161.12 196.37,-1170.74 201.41,-1165.88"/>
</g>
<!-- 36&#45;&gt;6 -->
<g id="edge10" class="edge">
<title>36&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M206.02,-898.7C205.14,-890.98 204.08,-881.71 203.1,-873.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="206.57,-872.64 201.95,-863.1 199.61,-873.44 206.57,-872.64"/>
</g>
<!-- 37&#45;&gt;36 -->
<g id="edge50" class="edge">
<title>37&#45;&gt;36</title>
<path fill="none" stroke="grey" stroke-width="2" d="M254.67,-970.7C247.24,-962.3 238.18,-952.07 230.02,-942.86"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="232.4,-940.27 223.15,-935.1 227.16,-944.91 232.4,-940.27"/>
</g>
<!-- 38&#45;&gt;3 -->
<g id="edge7" class="edge">
<title>38&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M191.97,-583.68C187.54,-573.48 182.29,-560.23 179,-548 154.47,-456.81 143.14,-344.85 138.98,-294.19"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="142.46,-293.76 138.18,-284.06 135.48,-294.31 142.46,-293.76"/>
</g>
<!-- 41 -->
<g id="node42" class="node">
<title>41</title>
<path fill="none" stroke="#80d856" stroke-width="2" d="M262,-548C262,-548 200,-548 200,-548 194,-548 188,-542 188,-536 188,-536 188,-519 188,-519 188,-513 194,-507 200,-507 200,-507 262,-507 262,-507 268,-507 274,-513 274,-519 274,-519 274,-536 274,-536 274,-542 268,-548 262,-548"/>
<text text-anchor="middle" x="231" y="-536" font-family="sans" font-size="10.00">get chr17&#39;s</text>
<text text-anchor="middle" x="231" y="-525" font-family="sans" font-size="10.00">sequence from</text>
<text text-anchor="middle" x="231" y="-514" font-family="sans" font-size="10.00">GRCh38</text>
</g>
<!-- 38&#45;&gt;41 -->
<g id="edge58" class="edge">
<title>38&#45;&gt;41</title>
<path fill="none" stroke="grey" stroke-width="2" d="M207.35,-583.82C210.71,-575.95 214.8,-566.4 218.62,-557.46"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="221.9,-558.69 222.61,-548.12 215.46,-555.94 221.9,-558.69"/>
</g>
<!-- 39 -->
<g id="node40" class="node">
<title>39</title>
<path fill="none" stroke="#d89556" stroke-width="2" d="M320,-383C320,-383 228,-383 228,-383 222,-383 216,-377 216,-371 216,-371 216,-332 216,-332 216,-326 222,-320 228,-320 228,-320 320,-320 320,-320 326,-320 332,-326 332,-332 332,-332 332,-371 332,-371 332,-377 326,-383 320,-383"/>
<text text-anchor="middle" x="274" y="-371" font-family="sans" font-size="10.00">plot alignment&#45;based</text>
<text text-anchor="middle" x="274" y="-360" font-family="sans" font-size="10.00">PHRED scores</text>
<text text-anchor="middle" x="274" y="-349" font-family="sans" font-size="10.00">for</text>
<text text-anchor="middle" x="274" y="-338" font-family="sans" font-size="10.00">SUP,corrected,duplex</text>
<text text-anchor="middle" x="274" y="-327" font-family="sans" font-size="10.00">reads</text>
</g>
<!-- 39&#45;&gt;3 -->
<g id="edge6" class="edge">
<title>39&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M223.76,-319.88C207.17,-309.77 189.03,-298.71 173.64,-289.33"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="175.3,-286.24 164.94,-284.03 171.65,-292.22 175.3,-286.24"/>
</g>
<!-- 40&#45;&gt;39 -->
<g id="edge54" class="edge">
<title>40&#45;&gt;39</title>
<path fill="none" stroke="grey" stroke-width="2" d="M284.17,-419C282.95,-411.01 281.57,-401.95 280.22,-393.15"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="283.64,-392.37 278.67,-383.02 276.72,-393.43 283.64,-392.37"/>
</g>
<!-- 41&#45;&gt;40 -->
<g id="edge55" class="edge">
<title>41&#45;&gt;40</title>
<path fill="none" stroke="grey" stroke-width="2" d="M245.09,-506.6C250.9,-498.4 257.78,-488.67 264.32,-479.44"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="267.27,-481.34 270.19,-471.16 261.55,-477.29 267.27,-481.34"/>
</g>
</g>
</svg>