test2.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<!-- 0 -->
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<title>0</title>
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<text text-anchor="middle" x="57" 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="57" y="-112" font-family="sans" font-size="10.00">convert GFA files</text>
<text text-anchor="middle" x="57" y="-101" font-family="sans" font-size="10.00"> to FASTA for</text>
<text text-anchor="middle" x="57" y="-90" font-family="sans" font-size="10.00">haplotypes</text>
<text text-anchor="middle" x="57" 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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<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
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<text text-anchor="middle" x="57" y="-200" font-family="sans" font-size="10.00">run final round</text>
<text text-anchor="middle" x="57" y="-189" font-family="sans" font-size="10.00"> of hifiasm with</text>
<text text-anchor="middle" x="57" y="-178" font-family="sans" font-size="10.00"> ultra&#45;long reads</text>
<text text-anchor="middle" x="57" 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>
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<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
<path fill="none" stroke="#c6d856" stroke-width="2" d="M112.5,-284C112.5,-284 77.5,-284 77.5,-284 71.5,-284 65.5,-278 65.5,-272 65.5,-272 65.5,-260 65.5,-260 65.5,-254 71.5,-248 77.5,-248 77.5,-248 112.5,-248 112.5,-248 118.5,-248 124.5,-254 124.5,-260 124.5,-260 124.5,-272 124.5,-272 124.5,-278 118.5,-284 112.5,-284"/>
<text text-anchor="middle" x="95" 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="M86.57,-247.69C82.8,-239.96 78.23,-230.57 73.81,-221.5"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="76.83,-219.71 69.3,-212.26 70.54,-222.78 76.83,-219.71"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
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<text text-anchor="middle" x="155" y="-740" font-family="sans" font-size="10.00">put shredded</text>
<text text-anchor="middle" x="155" y="-729" font-family="sans" font-size="10.00">reads back</text>
<text text-anchor="middle" x="155" y="-718" font-family="sans" font-size="10.00">together</text>
<text text-anchor="middle" x="155" y="-707" font-family="sans" font-size="10.00">then run hifiasm with</text>
<text text-anchor="middle" x="155" y="-696" font-family="sans" font-size="10.00">defaults to get</text>
<text text-anchor="middle" x="155" y="-685" font-family="sans" font-size="10.00">another 3 rounds</text>
<text text-anchor="middle" x="155" y="-674" font-family="sans" font-size="10.00">of error&#45;corrected</text>
<text text-anchor="middle" x="155" y="-663" font-family="sans" font-size="10.00">reads</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge6" class="edge">
<title>4&#45;&gt;3</title>
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<!-- 40 -->
<g id="node41" class="node">
<title>40</title>
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<text text-anchor="middle" x="155" y="-605" font-family="sans" font-size="10.00">run hifiasm to</text>
<text text-anchor="middle" x="155" y="-594" font-family="sans" font-size="10.00">get overlaps</text>
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<!-- 4&#45;&gt;40 -->
<g id="edge55" class="edge">
<title>4&#45;&gt;40</title>
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<!-- 42 -->
<g id="node43" class="node">
<title>42</title>
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<text text-anchor="middle" x="245" y="-459" font-family="sans" font-size="10.00">run mm2&#45;fast</text>
<text text-anchor="middle" x="245" y="-448" font-family="sans" font-size="10.00">to get alignment</text>
<text text-anchor="middle" x="245" y="-437" font-family="sans" font-size="10.00"> error&#45;rates to</text>
<text text-anchor="middle" x="245" y="-426" font-family="sans" font-size="10.00"> chr17</text>
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<!-- 4&#45;&gt;42 -->
<g id="edge58" class="edge">
<title>4&#45;&gt;42</title>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
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<text text-anchor="middle" x="155" y="-803.5" 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>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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<text text-anchor="middle" x="155" y="-881" font-family="sans" font-size="10.00">error&#45;correct the</text>
<text text-anchor="middle" x="155" y="-870" 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>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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<text text-anchor="middle" x="132" y="-1105" font-family="sans" font-size="10.00">make a sequence</text>
<text text-anchor="middle" x="132" y="-1094" font-family="sans" font-size="10.00">database for the</text>
<text text-anchor="middle" x="132" y="-1083" font-family="sans" font-size="10.00">2x corrected HiFi reads</text>
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<!-- 7&#45;&gt;6 -->
<g id="edge10" class="edge">
<title>7&#45;&gt;6</title>
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<!-- 38 -->
<g id="node39" class="node">
<title>38</title>
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<text text-anchor="middle" x="167" y="-953" font-family="sans" font-size="10.00">overlap the 2x</text>
<text text-anchor="middle" x="167" y="-942" font-family="sans" font-size="10.00">corrected reads</text>
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<!-- 7&#45;&gt;38 -->
<g id="edge53" class="edge">
<title>7&#45;&gt;38</title>
<path fill="none" stroke="grey" stroke-width="2" d="M135.58,-1075.75C139.07,-1057.14 144.76,-1028.53 151,-1004 153.19,-995.39 155.88,-986.09 158.43,-977.72"/>
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<!-- 39 -->
<g id="node40" class="node">
<title>39</title>
<path fill="none" stroke="#56d8a2" stroke-width="2" d="M285.5,-1040C285.5,-1040 172.5,-1040 172.5,-1040 166.5,-1040 160.5,-1034 160.5,-1028 160.5,-1028 160.5,-1016 160.5,-1016 160.5,-1010 166.5,-1004 172.5,-1004 172.5,-1004 285.5,-1004 285.5,-1004 291.5,-1004 297.5,-1010 297.5,-1016 297.5,-1016 297.5,-1028 297.5,-1028 297.5,-1034 291.5,-1040 285.5,-1040"/>
<text text-anchor="middle" x="229" y="-1025" font-family="sans" font-size="10.00">make a shimmer index</text>
<text text-anchor="middle" x="229" y="-1014" font-family="sans" font-size="10.00">for the 2x corrected reads</text>
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<!-- 7&#45;&gt;39 -->
<g id="edge54" class="edge">
<title>7&#45;&gt;39</title>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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<text text-anchor="middle" x="132" y="-1182" font-family="sans" font-size="10.00">make a file listing</text>
<text text-anchor="middle" x="132" y="-1171" font-family="sans" font-size="10.00">the locations of the</text>
<text text-anchor="middle" x="132" y="-1160" 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="M132,-1152.79C132,-1144.96 132,-1135.77 132,-1127.16"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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<text text-anchor="middle" x="130" y="-1317.5" font-family="sans" font-size="10.00">compress 2x corrected reads</text>
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<!-- 9&#45;&gt;8 -->
<g id="edge13" class="edge">
<title>9&#45;&gt;8</title>
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<!-- 37 -->
<g id="node38" class="node">
<title>37</title>
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<text text-anchor="middle" x="201" y="-1251" font-family="sans" font-size="10.00">compress 2nd</text>
<text text-anchor="middle" x="201" y="-1240" font-family="sans" font-size="10.00">set of overlaps</text>
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<!-- 9&#45;&gt;37 -->
<g id="edge51" class="edge">
<title>9&#45;&gt;37</title>
<path fill="none" stroke="grey" stroke-width="2" d="M147.55,-1301.7C156.23,-1293.14 166.86,-1282.66 176.35,-1273.3"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
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<text text-anchor="middle" x="130" y="-1395" font-family="sans" font-size="10.00">error&#45;correct the</text>
<text text-anchor="middle" x="130" y="-1384" 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>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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<text text-anchor="middle" x="136" y="-1611" font-family="sans" font-size="10.00">make a sequence database</text>
<text text-anchor="middle" x="136" y="-1600" 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="M135.52,-1589.85C134.48,-1552.83 132.02,-1465.18 130.77,-1420.39"/>
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<!-- 35 -->
<g id="node36" class="node">
<title>35</title>
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<text text-anchor="middle" x="201" y="-1467" font-family="sans" font-size="10.00">overlap the 1x</text>
<text text-anchor="middle" x="201" y="-1456" font-family="sans" font-size="10.00">corrected reads</text>
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<!-- 11&#45;&gt;35 -->
<g id="edge47" class="edge">
<title>11&#45;&gt;35</title>
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<!-- 36 -->
<g id="node37" class="node">
<title>36</title>
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<text text-anchor="middle" x="233" y="-1539" font-family="sans" font-size="10.00">make a shimmer index</text>
<text text-anchor="middle" x="233" y="-1528" font-family="sans" font-size="10.00">for the 1x corrected reads</text>
</g>
<!-- 11&#45;&gt;36 -->
<g id="edge49" class="edge">
<title>11&#45;&gt;36</title>
<path fill="none" stroke="grey" stroke-width="2" d="M159.98,-1589.7C172.31,-1580.8 187.52,-1569.82 200.85,-1560.2"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="203.24,-1562.79 209.3,-1554.1 199.14,-1557.12 203.24,-1562.79"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
<path fill="none" stroke="#68d856" stroke-width="2" d="M191.5,-1703C191.5,-1703 80.5,-1703 80.5,-1703 74.5,-1703 68.5,-1697 68.5,-1691 68.5,-1691 68.5,-1674 68.5,-1674 68.5,-1668 74.5,-1662 80.5,-1662 80.5,-1662 191.5,-1662 191.5,-1662 197.5,-1662 203.5,-1668 203.5,-1674 203.5,-1674 203.5,-1691 203.5,-1691 203.5,-1697 197.5,-1703 191.5,-1703"/>
<text text-anchor="middle" x="136" y="-1691" font-family="sans" font-size="10.00">make a file listing</text>
<text text-anchor="middle" x="136" y="-1680" font-family="sans" font-size="10.00">the locations of</text>
<text text-anchor="middle" x="136" y="-1669" 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="M136,-1661.69C136,-1653.91 136,-1644.84 136,-1636.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="139.5,-1636.32 136,-1626.32 132.5,-1636.32 139.5,-1636.32"/>
</g>
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
<path fill="none" stroke="#b6d856" stroke-width="2" d="M135.5,-1775C135.5,-1775 70.5,-1775 70.5,-1775 64.5,-1775 58.5,-1769 58.5,-1763 58.5,-1763 58.5,-1751 58.5,-1751 58.5,-1745 64.5,-1739 70.5,-1739 70.5,-1739 135.5,-1739 135.5,-1739 141.5,-1739 147.5,-1745 147.5,-1751 147.5,-1751 147.5,-1763 147.5,-1763 147.5,-1769 141.5,-1775 135.5,-1775"/>
<text text-anchor="middle" x="103" y="-1760" font-family="sans" font-size="10.00">compress 1x</text>
<text text-anchor="middle" x="103" y="-1749" 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="M110.82,-1738.82C114.4,-1730.95 118.75,-1721.4 122.82,-1712.46"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="126.11,-1713.67 127.07,-1703.12 119.74,-1710.77 126.11,-1713.67"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
<path fill="none" stroke="#d87556" stroke-width="2" d="M167.5,-1847C167.5,-1847 68.5,-1847 68.5,-1847 62.5,-1847 56.5,-1841 56.5,-1835 56.5,-1835 56.5,-1823 56.5,-1823 56.5,-1817 62.5,-1811 68.5,-1811 68.5,-1811 167.5,-1811 167.5,-1811 173.5,-1811 179.5,-1817 179.5,-1823 179.5,-1823 179.5,-1835 179.5,-1835 179.5,-1841 173.5,-1847 167.5,-1847"/>
<text text-anchor="middle" x="118" y="-1826.5" 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="M114.29,-1810.7C112.64,-1802.98 110.65,-1793.71 108.81,-1785.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="112.18,-1784.15 106.67,-1775.1 105.34,-1785.62 112.18,-1784.15"/>
</g>
<!-- 34 -->
<g id="node35" class="node">
<title>34</title>
<path fill="none" stroke="#569ad8" stroke-width="2" d="M238.5,-1775C238.5,-1775 177.5,-1775 177.5,-1775 171.5,-1775 165.5,-1769 165.5,-1763 165.5,-1763 165.5,-1751 165.5,-1751 165.5,-1745 171.5,-1739 177.5,-1739 177.5,-1739 238.5,-1739 238.5,-1739 244.5,-1739 250.5,-1745 250.5,-1751 250.5,-1751 250.5,-1763 250.5,-1763 250.5,-1769 244.5,-1775 238.5,-1775"/>
<text text-anchor="middle" x="208" y="-1760" font-family="sans" font-size="10.00">compress 1st</text>
<text text-anchor="middle" x="208" y="-1749" font-family="sans" font-size="10.00">set of overlaps</text>
</g>
<!-- 14&#45;&gt;34 -->
<g id="edge46" class="edge">
<title>14&#45;&gt;34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M140.25,-1810.7C151.58,-1801.88 165.53,-1791.03 177.82,-1781.47"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="180.26,-1784.01 186.01,-1775.1 175.97,-1778.48 180.26,-1784.01"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
<path fill="none" stroke="#88d856" stroke-width="2" d="M202.5,-2063C202.5,-2063 105.5,-2063 105.5,-2063 99.5,-2063 93.5,-2057 93.5,-2051 93.5,-2051 93.5,-2039 93.5,-2039 93.5,-2033 99.5,-2027 105.5,-2027 105.5,-2027 202.5,-2027 202.5,-2027 208.5,-2027 214.5,-2033 214.5,-2039 214.5,-2039 214.5,-2051 214.5,-2051 214.5,-2057 208.5,-2063 202.5,-2063"/>
<text text-anchor="middle" x="154" y="-2048" font-family="sans" font-size="10.00">make a sequence</text>
<text text-anchor="middle" x="154" y="-2037" 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="M151.11,-2026.85C144.87,-1989.75 130.08,-1901.81 122.56,-1857.1"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="126.01,-1856.51 120.9,-1847.23 119.11,-1857.67 126.01,-1856.51"/>
</g>
<!-- 32 -->
<g id="node33" class="node">
<title>32</title>
<path fill="none" stroke="#ced856" stroke-width="2" d="M238,-1919C238,-1919 164,-1919 164,-1919 158,-1919 152,-1913 152,-1907 152,-1907 152,-1895 152,-1895 152,-1889 158,-1883 164,-1883 164,-1883 238,-1883 238,-1883 244,-1883 250,-1889 250,-1895 250,-1895 250,-1907 250,-1907 250,-1913 244,-1919 238,-1919"/>
<text text-anchor="middle" x="201" y="-1898.5" font-family="sans" font-size="10.00">overlap the reads</text>
</g>
<!-- 15&#45;&gt;32 -->
<g id="edge42" class="edge">
<title>15&#45;&gt;32</title>
<path fill="none" stroke="grey" stroke-width="2" d="M156.22,-2026.88C158.91,-2008.67 164.21,-1979.21 173,-1955 176.3,-1945.9 180.9,-1936.42 185.42,-1928.03"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="188.58,-1929.55 190.41,-1919.11 182.47,-1926.13 188.58,-1929.55"/>
</g>
<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
<path fill="none" stroke="#97d856" stroke-width="2" d="M290,-1991C290,-1991 194,-1991 194,-1991 188,-1991 182,-1985 182,-1979 182,-1979 182,-1967 182,-1967 182,-1961 188,-1955 194,-1955 194,-1955 290,-1955 290,-1955 296,-1955 302,-1961 302,-1967 302,-1967 302,-1979 302,-1979 302,-1985 296,-1991 290,-1991"/>
<text text-anchor="middle" x="242" y="-1976" font-family="sans" font-size="10.00">make a shimmer index</text>
<text text-anchor="middle" x="242" y="-1965" font-family="sans" font-size="10.00">for the reads</text>
</g>
<!-- 15&#45;&gt;33 -->
<g id="edge44" class="edge">
<title>15&#45;&gt;33</title>
<path fill="none" stroke="grey" stroke-width="2" d="M175.75,-2026.7C186.84,-2017.88 200.47,-2007.03 212.49,-1997.47"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="214.85,-2000.07 220.5,-1991.1 210.49,-1994.59 214.85,-2000.07"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
<path fill="none" stroke="#d8a456" stroke-width="2" d="M225.5,-2151C225.5,-2151 82.5,-2151 82.5,-2151 76.5,-2151 70.5,-2145 70.5,-2139 70.5,-2139 70.5,-2111 70.5,-2111 70.5,-2105 76.5,-2099 82.5,-2099 82.5,-2099 225.5,-2099 225.5,-2099 231.5,-2099 237.5,-2105 237.5,-2111 237.5,-2111 237.5,-2139 237.5,-2139 237.5,-2145 231.5,-2151 225.5,-2151"/>
<text text-anchor="middle" x="154" y="-2139" font-family="sans" font-size="10.00">make a file listing</text>
<text text-anchor="middle" x="154" y="-2128" font-family="sans" font-size="10.00">the location of the</text>
<text text-anchor="middle" x="154" y="-2117" font-family="sans" font-size="10.00">racon/brutal_rewrite/kmer_filter</text>
<text text-anchor="middle" x="154" y="-2106" 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="M154,-2098.89C154,-2090.84 154,-2081.88 154,-2073.66"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="157.5,-2073.41 154,-2063.41 150.5,-2073.41 157.5,-2073.41"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
<path fill="none" stroke="#56d892" stroke-width="2" d="M186.5,-2239C186.5,-2239 121.5,-2239 121.5,-2239 115.5,-2239 109.5,-2233 109.5,-2227 109.5,-2227 109.5,-2199 109.5,-2199 109.5,-2193 115.5,-2187 121.5,-2187 121.5,-2187 186.5,-2187 186.5,-2187 192.5,-2187 198.5,-2193 198.5,-2199 198.5,-2199 198.5,-2227 198.5,-2227 198.5,-2233 192.5,-2239 186.5,-2239"/>
<text text-anchor="middle" x="154" y="-2227" font-family="sans" font-size="10.00">put all 8</text>
<text text-anchor="middle" x="154" y="-2216" font-family="sans" font-size="10.00">files of</text>
<text text-anchor="middle" x="154" y="-2205" font-family="sans" font-size="10.00">shredded reads</text>
<text text-anchor="middle" x="154" y="-2194" 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="M154,-2186.66C154,-2178.7 154,-2169.76 154,-2161.24"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="157.5,-2161.16 154,-2151.16 150.5,-2161.16 157.5,-2161.16"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
<path fill="none" stroke="#56c1d8" stroke-width="2" d="M177.5,-2316C177.5,-2316 130.5,-2316 130.5,-2316 124.5,-2316 118.5,-2310 118.5,-2304 118.5,-2304 118.5,-2287 118.5,-2287 118.5,-2281 124.5,-2275 130.5,-2275 130.5,-2275 177.5,-2275 177.5,-2275 183.5,-2275 189.5,-2281 189.5,-2287 189.5,-2287 189.5,-2304 189.5,-2304 189.5,-2310 183.5,-2316 177.5,-2316"/>
<text text-anchor="middle" x="154" y="-2304" font-family="sans" font-size="10.00">shred reads</text>
<text text-anchor="middle" x="154" y="-2293" font-family="sans" font-size="10.00">into pieces</text>
<text text-anchor="middle" x="154" y="-2282" 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="M154,-2274.6C154,-2266.99 154,-2258.06 154,-2249.43"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="157.5,-2249.16 154,-2239.16 150.5,-2249.16 157.5,-2249.16"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
<path fill="none" stroke="#56d8b9" stroke-width="2" d="M182,-2393C182,-2393 126,-2393 126,-2393 120,-2393 114,-2387 114,-2381 114,-2381 114,-2364 114,-2364 114,-2358 120,-2352 126,-2352 126,-2352 182,-2352 182,-2352 188,-2352 194,-2358 194,-2364 194,-2364 194,-2381 194,-2381 194,-2387 188,-2393 182,-2393"/>
<text text-anchor="middle" x="154" y="-2381" font-family="sans" font-size="10.00">split reads</text>
<text text-anchor="middle" x="154" y="-2370" font-family="sans" font-size="10.00">into 8 files</text>
<text text-anchor="middle" x="154" y="-2359" 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="M154,-2351.79C154,-2343.96 154,-2334.77 154,-2326.16"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="157.5,-2326.07 154,-2316.07 150.5,-2326.07 157.5,-2326.07"/>
</g>
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
<path fill="none" stroke="#56a9d8" stroke-width="2" d="M205.5,-2470C205.5,-2470 102.5,-2470 102.5,-2470 96.5,-2470 90.5,-2464 90.5,-2458 90.5,-2458 90.5,-2441 90.5,-2441 90.5,-2435 96.5,-2429 102.5,-2429 102.5,-2429 205.5,-2429 205.5,-2429 211.5,-2429 217.5,-2435 217.5,-2441 217.5,-2441 217.5,-2458 217.5,-2458 217.5,-2464 211.5,-2470 205.5,-2470"/>
<text text-anchor="middle" x="154" y="-2458" font-family="sans" font-size="10.00">error&#45;correct reads</text>
<text text-anchor="middle" x="154" y="-2447" font-family="sans" font-size="10.00">with overlap info with</text>
<text text-anchor="middle" x="154" y="-2436" font-family="sans" font-size="10.00">racon from vechat again</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="M154,-2428.79C154,-2420.96 154,-2411.77 154,-2403.16"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="157.5,-2403.07 154,-2393.07 150.5,-2403.07 157.5,-2403.07"/>
</g>
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
<path fill="none" stroke="#d8cb56" stroke-width="2" d="M194.5,-2679C194.5,-2679 81.5,-2679 81.5,-2679 75.5,-2679 69.5,-2673 69.5,-2667 69.5,-2667 69.5,-2639 69.5,-2639 69.5,-2633 75.5,-2627 81.5,-2627 81.5,-2627 194.5,-2627 194.5,-2627 200.5,-2627 206.5,-2633 206.5,-2639 206.5,-2639 206.5,-2667 206.5,-2667 206.5,-2673 200.5,-2679 194.5,-2679"/>
<text text-anchor="middle" x="138" y="-2667" font-family="sans" font-size="10.00">remove any</text>
<text text-anchor="middle" x="138" y="-2656" font-family="sans" font-size="10.00">duplicated read identifiers</text>
<text text-anchor="middle" x="138" y="-2645" font-family="sans" font-size="10.00">if any from</text>
<text text-anchor="middle" x="138" y="-2634" font-family="sans" font-size="10.00">1st racon run</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="M132.36,-2626.89C126.72,-2597.55 120.04,-2547.71 129,-2506 130.95,-2496.92 134.51,-2487.53 138.34,-2479.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="141.5,-2480.62 142.72,-2470.09 135.2,-2477.57 141.5,-2480.62"/>
</g>
<!-- 31 -->
<g id="node32" class="node">
<title>31</title>
<path fill="none" stroke="#56d873" stroke-width="2" d="M239.5,-2591C239.5,-2591 150.5,-2591 150.5,-2591 144.5,-2591 138.5,-2585 138.5,-2579 138.5,-2579 138.5,-2518 138.5,-2518 138.5,-2512 144.5,-2506 150.5,-2506 150.5,-2506 239.5,-2506 239.5,-2506 245.5,-2506 251.5,-2512 251.5,-2518 251.5,-2518 251.5,-2579 251.5,-2579 251.5,-2585 245.5,-2591 239.5,-2591"/>
<text text-anchor="middle" x="195" y="-2579" font-family="sans" font-size="10.00">use mm2&#45;fast</text>
<text text-anchor="middle" x="195" y="-2568" font-family="sans" font-size="10.00">to overlap SUP reads</text>
<text text-anchor="middle" x="195" y="-2557" font-family="sans" font-size="10.00">and filter overlaps</text>
<text text-anchor="middle" x="195" y="-2546" font-family="sans" font-size="10.00">with awk and fpa</text>
<text text-anchor="middle" x="195" y="-2535" font-family="sans" font-size="10.00">again</text>
<text text-anchor="middle" x="195" y="-2524" font-family="sans" font-size="10.00">but more</text>
<text text-anchor="middle" x="195" y="-2513" font-family="sans" font-size="10.00">stringently</text>
</g>
<!-- 21&#45;&gt;31 -->
<g id="edge41" class="edge">
<title>21&#45;&gt;31</title>
<path fill="none" stroke="grey" stroke-width="2" d="M151.94,-2626.93C156.49,-2618.75 161.71,-2609.36 166.91,-2600.01"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="170.07,-2601.53 171.87,-2591.09 163.95,-2598.13 170.07,-2601.53"/>
</g>
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
<path fill="none" stroke="#d89c56" stroke-width="2" d="M171,-2756C171,-2756 105,-2756 105,-2756 99,-2756 93,-2750 93,-2744 93,-2744 93,-2727 93,-2727 93,-2721 99,-2715 105,-2715 105,-2715 171,-2715 171,-2715 177,-2715 183,-2721 183,-2727 183,-2727 183,-2744 183,-2744 183,-2750 177,-2756 171,-2756"/>
<text text-anchor="middle" x="138" y="-2744" font-family="sans" font-size="10.00">k&#45;mer filtering </text>
<text text-anchor="middle" x="138" y="-2733" font-family="sans" font-size="10.00">of bad reads </text>
<text text-anchor="middle" x="138" y="-2722" font-family="sans" font-size="10.00">with kmer_filter</text>
</g>
<!-- 22&#45;&gt;21 -->
<g id="edge31" class="edge">
<title>22&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M138,-2714.6C138,-2706.99 138,-2698.06 138,-2689.43"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="141.5,-2689.16 138,-2679.16 134.5,-2689.16 141.5,-2689.16"/>
</g>
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
<path fill="none" stroke="#56d8a9" stroke-width="2" d="M187,-2828C187,-2828 89,-2828 89,-2828 83,-2828 77,-2822 77,-2816 77,-2816 77,-2804 77,-2804 77,-2798 83,-2792 89,-2792 89,-2792 187,-2792 187,-2792 193,-2792 199,-2798 199,-2804 199,-2804 199,-2816 199,-2816 199,-2822 193,-2828 187,-2828"/>
<text text-anchor="middle" x="138" y="-2813" font-family="sans" font-size="10.00">k&#45;mer error&#45;correction</text>
<text text-anchor="middle" x="138" y="-2802" font-family="sans" font-size="10.00">with brutal rewrite</text>
</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="M138,-2791.82C138,-2784.2 138,-2775 138,-2766.32"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="141.5,-2766.12 138,-2756.12 134.5,-2766.12 141.5,-2766.12"/>
</g>
<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
<path fill="none" stroke="#70d856" stroke-width="2" d="M184,-2905C184,-2905 92,-2905 92,-2905 86,-2905 80,-2899 80,-2893 80,-2893 80,-2876 80,-2876 80,-2870 86,-2864 92,-2864 92,-2864 184,-2864 184,-2864 190,-2864 196,-2870 196,-2876 196,-2876 196,-2893 196,-2893 196,-2899 190,-2905 184,-2905"/>
<text text-anchor="middle" x="138" y="-2893" font-family="sans" font-size="10.00">error&#45;correct reads</text>
<text text-anchor="middle" x="138" y="-2882" font-family="sans" font-size="10.00">with overlap info with</text>
<text text-anchor="middle" x="138" y="-2871" font-family="sans" font-size="10.00">racon from vechat</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="M138,-2863.69C138,-2855.91 138,-2846.84 138,-2838.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="141.5,-2838.32 138,-2828.32 134.5,-2838.32 141.5,-2838.32"/>
</g>
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
<path fill="none" stroke="#d86e56" stroke-width="2" d="M172,-3065C172,-3065 116,-3065 116,-3065 110,-3065 104,-3059 104,-3053 104,-3053 104,-3041 104,-3041 104,-3035 110,-3029 116,-3029 116,-3029 172,-3029 172,-3029 178,-3029 184,-3035 184,-3041 184,-3041 184,-3053 184,-3053 184,-3059 178,-3065 172,-3065"/>
<text text-anchor="middle" x="144" y="-3050" font-family="sans" font-size="10.00">convert bam</text>
<text text-anchor="middle" x="144" y="-3039" font-family="sans" font-size="10.00">files to FASTQ</text>
</g>
<!-- 25&#45;&gt;2 -->
<g id="edge4" class="edge">
<title>25&#45;&gt;2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M120.25,-3028.99C86.31,-3002.5 28,-2947.9 28,-2885.5 28,-2885.5 28,-2885.5 28,-350.5 28,-305.76 38.66,-255.17 47.05,-222.27"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="50.53,-222.8 49.68,-212.24 43.76,-221.03 50.53,-222.8"/>
</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="M134.46,-3028.93C129.36,-3018.82 123.61,-3005.57 121,-2993 116.3,-2970.37 117.58,-2963.86 121,-2941 122.29,-2932.36 124.66,-2923.2 127.23,-2914.87"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="130.61,-2915.8 130.4,-2905.21 123.96,-2913.62 130.61,-2915.8"/>
</g>
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
<path fill="none" stroke="#56d85b" stroke-width="2" d="M231.5,-2993C231.5,-2993 142.5,-2993 142.5,-2993 136.5,-2993 130.5,-2987 130.5,-2981 130.5,-2981 130.5,-2953 130.5,-2953 130.5,-2947 136.5,-2941 142.5,-2941 142.5,-2941 231.5,-2941 231.5,-2941 237.5,-2941 243.5,-2947 243.5,-2953 243.5,-2953 243.5,-2981 243.5,-2981 243.5,-2987 237.5,-2993 231.5,-2993"/>
<text text-anchor="middle" x="187" y="-2981" font-family="sans" font-size="10.00">use mm2&#45;fast</text>
<text text-anchor="middle" x="187" y="-2970" font-family="sans" font-size="10.00">to overlap SUP reads</text>
<text text-anchor="middle" x="187" y="-2959" font-family="sans" font-size="10.00">and filter overlaps</text>
<text text-anchor="middle" x="187" y="-2948" font-family="sans" font-size="10.00">with awk and fpa</text>
</g>
<!-- 25&#45;&gt;30 -->
<g id="edge40" class="edge">
<title>25&#45;&gt;30</title>
<path fill="none" stroke="grey" stroke-width="2" d="M153.54,-3028.69C157.85,-3020.88 163.09,-3011.37 168.14,-3002.22"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="171.31,-3003.7 173.08,-2993.26 165.18,-3000.32 171.31,-3003.7"/>
</g>
<!-- 25&#45;&gt;42 -->
<g id="edge59" class="edge">
<title>25&#45;&gt;42</title>
<path fill="none" stroke="grey" stroke-width="2" d="M184.36,-3031.9C239.06,-3009.9 330,-2961.85 330,-2885.5 330,-2885.5 330,-2885.5 330,-601 330,-554.43 300.14,-508.61 275.81,-479.02"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="278.26,-476.49 269.13,-471.11 272.91,-481.01 278.26,-476.49"/>
</g>
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
<path fill="none" stroke="#56d8d8" stroke-width="2" d="M202,-3137C202,-3137 86,-3137 86,-3137 80,-3137 74,-3131 74,-3125 74,-3125 74,-3113 74,-3113 74,-3107 80,-3101 86,-3101 86,-3101 202,-3101 202,-3101 208,-3101 214,-3107 214,-3113 214,-3113 214,-3125 214,-3125 214,-3131 208,-3137 202,-3137"/>
<text text-anchor="middle" x="144" y="-3122" font-family="sans" font-size="10.00">use dorado to basecall</text>
<text text-anchor="middle" x="144" y="-3111" font-family="sans" font-size="10.00">squiggles using SUP model</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="M144,-3100.7C144,-3092.98 144,-3083.71 144,-3075.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="147.5,-3075.1 144,-3065.1 140.5,-3075.1 147.5,-3075.1"/>
</g>
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
<path fill="none" stroke="#d85e56" stroke-width="2" d="M226,-3209C226,-3209 62,-3209 62,-3209 56,-3209 50,-3203 50,-3197 50,-3197 50,-3185 50,-3185 50,-3179 56,-3173 62,-3173 62,-3173 226,-3173 226,-3173 232,-3173 238,-3179 238,-3185 238,-3185 238,-3197 238,-3197 238,-3203 232,-3209 226,-3209"/>
<text text-anchor="middle" x="144" y="-3194" font-family="sans" font-size="10.00">use blue_crab to convert</text>
<text text-anchor="middle" x="144" y="-3183" font-family="sans" font-size="10.00">squiggles from blow5 to pod5 format</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="M144,-3172.7C144,-3164.98 144,-3155.71 144,-3147.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="147.5,-3147.1 144,-3137.1 140.5,-3147.1 147.5,-3147.1"/>
</g>
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
<path fill="none" stroke="#5663d8" stroke-width="2" d="M197,-3286C197,-3286 91,-3286 91,-3286 85,-3286 79,-3280 79,-3274 79,-3274 79,-3257 79,-3257 79,-3251 85,-3245 91,-3245 91,-3245 197,-3245 197,-3245 203,-3245 209,-3251 209,-3257 209,-3257 209,-3274 209,-3274 209,-3280 203,-3286 197,-3286"/>
<text text-anchor="middle" x="144" y="-3274" font-family="sans" font-size="10.00">use slow5tools to extract</text>
<text text-anchor="middle" x="144" y="-3263" font-family="sans" font-size="10.00">squiggles for desired</text>
<text text-anchor="middle" x="144" y="-3252" font-family="sans" font-size="10.00">chr17 reads</text>
</g>
<!-- 28&#45;&gt;27 -->
<g id="edge38" class="edge">
<title>28&#45;&gt;27</title>
<path fill="none" stroke="grey" stroke-width="2" d="M144,-3244.69C144,-3236.91 144,-3227.84 144,-3219.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="147.5,-3219.32 144,-3209.32 140.5,-3219.32 147.5,-3219.32"/>
</g>
<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
<path fill="none" stroke="#d8b456" stroke-width="2" d="M203,-3385C203,-3385 85,-3385 85,-3385 79,-3385 73,-3379 73,-3373 73,-3373 73,-3334 73,-3334 73,-3328 79,-3322 85,-3322 85,-3322 203,-3322 203,-3322 209,-3322 215,-3328 215,-3334 215,-3334 215,-3373 215,-3373 215,-3379 209,-3385 203,-3385"/>
<text text-anchor="middle" x="144" y="-3373" font-family="sans" font-size="10.00">filter gaf file for</text>
<text text-anchor="middle" x="144" y="-3362" font-family="sans" font-size="10.00">desired chromosome reads</text>
<text text-anchor="middle" x="144" y="-3351" font-family="sans" font-size="10.00">in this</text>
<text text-anchor="middle" x="144" y="-3340" font-family="sans" font-size="10.00">example:</text>
<text text-anchor="middle" x="144" y="-3329" font-family="sans" font-size="10.00">chr17</text>
</g>
<!-- 29&#45;&gt;28 -->
<g id="edge39" class="edge">
<title>29&#45;&gt;28</title>
<path fill="none" stroke="grey" stroke-width="2" d="M144,-3321.94C144,-3313.59 144,-3304.55 144,-3296.25"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="147.5,-3296.23 144,-3286.23 140.5,-3296.23 147.5,-3296.23"/>
</g>
<!-- 30&#45;&gt;24 -->
<g id="edge34" class="edge">
<title>30&#45;&gt;24</title>
<path fill="none" stroke="grey" stroke-width="2" d="M171.76,-2940.97C166.55,-2932.41 160.68,-2922.76 155.32,-2913.95"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="158.15,-2911.87 149.96,-2905.15 152.17,-2915.51 158.15,-2911.87"/>
</g>
<!-- 31&#45;&gt;20 -->
<g id="edge30" class="edge">
<title>31&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M177.37,-2505.8C173.6,-2496.87 169.69,-2487.62 166.18,-2479.31"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="169.38,-2477.9 162.26,-2470.05 162.93,-2480.62 169.38,-2477.9"/>
</g>
<!-- 32&#45;&gt;14 -->
<g id="edge22" class="edge">
<title>32&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M180.48,-1882.7C170.13,-1873.97 157.41,-1863.24 146.16,-1853.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="148.18,-1850.88 138.28,-1847.1 143.67,-1856.23 148.18,-1850.88"/>
</g>
<!-- 32&#45;&gt;34 -->
<g id="edge45" class="edge">
<title>32&#45;&gt;34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M201.84,-1882.87C203.04,-1858.67 205.23,-1814.21 206.65,-1785.39"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="210.16,-1785.35 207.15,-1775.19 203.16,-1785 210.16,-1785.35"/>
</g>
<!-- 33&#45;&gt;32 -->
<g id="edge43" class="edge">
<title>33&#45;&gt;32</title>
<path fill="none" stroke="grey" stroke-width="2" d="M231.87,-1954.7C227.15,-1946.64 221.44,-1936.89 216.22,-1927.98"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="219.09,-1925.96 211.02,-1919.1 213.05,-1929.5 219.09,-1925.96"/>
</g>
<!-- 34&#45;&gt;12 -->
<g id="edge20" class="edge">
<title>34&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M190.94,-1738.82C182.54,-1730.36 172.21,-1719.97 162.79,-1710.48"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="165.01,-1707.75 155.48,-1703.12 160.05,-1712.68 165.01,-1707.75"/>
</g>
<!-- 35&#45;&gt;10 -->
<g id="edge16" class="edge">
<title>35&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M183.45,-1445.7C174.77,-1437.14 164.14,-1426.66 154.65,-1417.3"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="156.93,-1414.63 147.35,-1410.1 152.01,-1419.62 156.93,-1414.63"/>
</g>
<!-- 35&#45;&gt;37 -->
<g id="edge50" class="edge">
<title>35&#45;&gt;37</title>
<path fill="none" stroke="grey" stroke-width="2" d="M204.41,-1445.57C209.74,-1415.99 218.82,-1354.09 213,-1302 212.04,-1293.43 210.24,-1284.22 208.31,-1275.93"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="211.66,-1274.89 205.87,-1266.02 204.87,-1276.57 211.66,-1274.89"/>
</g>
<!-- 36&#45;&gt;35 -->
<g id="edge48" class="edge">
<title>36&#45;&gt;35</title>
<path fill="none" stroke="grey" stroke-width="2" d="M225.09,-1517.7C221.45,-1509.73 217.05,-1500.1 213.01,-1491.26"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="216.16,-1489.74 208.82,-1482.1 209.79,-1492.65 216.16,-1489.74"/>
</g>
<!-- 37&#45;&gt;8 -->
<g id="edge14" class="edge">
<title>37&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M184.65,-1229.82C176.6,-1221.36 166.7,-1210.97 157.68,-1201.48"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="160.1,-1198.95 150.67,-1194.12 155.03,-1203.78 160.1,-1198.95"/>
</g>
<!-- 38&#45;&gt;6 -->
<g id="edge11" class="edge">
<title>38&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M164.03,-931.7C162.71,-923.98 161.12,-914.71 159.65,-906.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="163.07,-905.37 157.93,-896.1 156.17,-906.55 163.07,-905.37"/>
</g>
<!-- 39&#45;&gt;38 -->
<g id="edge52" class="edge">
<title>39&#45;&gt;38</title>
<path fill="none" stroke="grey" stroke-width="2" d="M213.67,-1003.7C206.24,-995.3 197.18,-985.07 189.02,-975.86"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="191.4,-973.27 182.15,-968.1 186.16,-977.91 191.4,-973.27"/>
</g>
<!-- 40&#45;&gt;3 -->
<g id="edge5" class="edge">
<title>40&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M148.2,-583.57C144.43,-573.34 139.93,-560.09 137,-548 114.8,-456.45 102.35,-345.1 97.46,-294.45"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="100.92,-293.94 96.5,-284.31 93.95,-294.6 100.92,-293.94"/>
</g>
<!-- 43 -->
<g id="node44" class="node">
<title>43</title>
<path fill="none" stroke="#56c9d8" stroke-width="2" d="M220,-548C220,-548 158,-548 158,-548 152,-548 146,-542 146,-536 146,-536 146,-519 146,-519 146,-513 152,-507 158,-507 158,-507 220,-507 220,-507 226,-507 232,-513 232,-519 232,-519 232,-536 232,-536 232,-542 226,-548 220,-548"/>
<text text-anchor="middle" x="189" y="-536" font-family="sans" font-size="10.00">get chr17&#39;s</text>
<text text-anchor="middle" x="189" y="-525" font-family="sans" font-size="10.00">sequence from</text>
<text text-anchor="middle" x="189" y="-514" font-family="sans" font-size="10.00">GRCh38</text>
</g>
<!-- 40&#45;&gt;43 -->
<g id="edge60" class="edge">
<title>40&#45;&gt;43</title>
<path fill="none" stroke="grey" stroke-width="2" d="M163.06,-583.82C166.79,-575.86 171.32,-566.19 175.55,-557.18"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="178.72,-558.66 179.8,-548.12 172.38,-555.69 178.72,-558.66"/>
</g>
<!-- 41 -->
<g id="node42" class="node">
<title>41</title>
<path fill="none" stroke="#d88d56" stroke-width="2" d="M276,-383C276,-383 186,-383 186,-383 180,-383 174,-377 174,-371 174,-371 174,-332 174,-332 174,-326 180,-320 186,-320 186,-320 276,-320 276,-320 282,-320 288,-326 288,-332 288,-332 288,-371 288,-371 288,-377 282,-383 276,-383"/>
<text text-anchor="middle" x="231" y="-371" font-family="sans" font-size="10.00">plot alignment&#45;based</text>
<text text-anchor="middle" x="231" y="-360" font-family="sans" font-size="10.00">PHRED scores</text>
<text text-anchor="middle" x="231" y="-349" font-family="sans" font-size="10.00">for</text>
<text text-anchor="middle" x="231" y="-338" font-family="sans" font-size="10.00">SUP &amp; corrected</text>
<text text-anchor="middle" x="231" y="-327" font-family="sans" font-size="10.00">reads</text>
</g>
<!-- 41&#45;&gt;3 -->
<g id="edge7" class="edge">
<title>41&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M181.13,-319.88C164.65,-309.77 146.65,-298.71 131.37,-289.33"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="133.08,-286.28 122.73,-284.03 129.42,-292.24 133.08,-286.28"/>
</g>
<!-- 42&#45;&gt;41 -->
<g id="edge56" class="edge">
<title>42&#45;&gt;41</title>
<path fill="none" stroke="grey" stroke-width="2" d="M241.17,-419C239.95,-411.01 238.57,-401.95 237.22,-393.15"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="240.64,-392.37 235.67,-383.02 233.72,-393.43 240.64,-392.37"/>
</g>
<!-- 43&#45;&gt;42 -->
<g id="edge57" class="edge">
<title>43&#45;&gt;42</title>
<path fill="none" stroke="grey" stroke-width="2" d="M202.84,-506.6C208.55,-498.4 215.31,-488.67 221.74,-479.44"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="224.66,-481.36 227.5,-471.16 218.92,-477.37 224.66,-481.36"/>
</g>
</g>
</svg>