View source for Hak-Min Kim KOREF

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<p><span style="font-size:20px"><strong>KOREF</strong></span></p>

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<p><strong><span style="font-size:16px">1. Raw data and project folder information</span></strong></p>

<ol style="list-style-type:upper-alpha">
	<li><span style="font-size:16px">Project folder:</span>

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		<li><span style="font-size:16px">KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/</span></li>
		<li><span style="font-size:16px">KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/</span></li>
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	<li><span style="font-size:16px">Raw data information: <a href="http://in.tgi.kr/index.php/Overall_Data_Information">http://in.tgi.kr/index.php/Overall_Data_Information</a></span></li>
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<p><span style="font-size:16px"><strong>2. Paper status</strong>: Published (</span><span style="font-size:16px"><a href="https://www.nature.com/articles/ncomms13637]">An&nbsp;ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.</a>&nbsp;<em>Nature communications</em>, 2016)</span></p>

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<p><strong><span style="font-size:16px">3. Analysis result</span></strong></p>

<ol style="list-style-type:upper-alpha">
	<li><span style="font-size:16px">Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly</span></li>
	<li><span style="font-size:16px">Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation</span>
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		<li><span style="font-size:16px">Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit</span></li>
		<li><span style="font-size:16px">Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask</span></li>
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	<li><span style="font-size:16px">Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly</span></li>
	<li><span style="font-size:16px">Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication</span></li>
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<p><strong><span style="font-size:16px">4. Related script</span></strong></p>

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	<li><span style="font-size:16px">Repeat maksing</span>

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		<li><span style="font-size:16px">Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl</span></li>
		<li><span style="font-size:16px">Count the hetero variants in repeat region: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/1_Count_hetero_variants_in_repeat_region_withArray.pl</span></li>
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	<li><span style="font-size:16px">Sspace_longread (scaffolding program)</span>
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		<li><span style="font-size:16px">Run Sspace_longread with Pacbio and Moleculo data: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly/3.Pacbio_Moleculo_SSPACE_with_2/script/0_SSPACE-longread_run_with_Pacbio_Moleculo.pl</span></li>
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	<li><span style="font-size:16px">Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl</span></li>
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<p><strong><span style="font-size:16px">5. Methods</span></strong></p>

<ol style="list-style-type:upper-alpha">
	<li>Assembly process<br />
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	<img alt="" src="/ckfinder/userfiles/images/5_KOREF_assembly_process.PNG" style="height:790px; width:700px" /><br />
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	<li><span style="font-size:16px">All methods are described in the method &amp; material section of the published article.</span></li>
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