quickload/S_chinensis_Apr_2019/HEADER.md

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<h1>Simmondsia chinensis (Apr 2019) Jojoba (sc1)</h1>
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The files listed below are formatted for visualization in the Integrated Genome Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
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The file named S_chinensis_Apr_2019.2bit contains sequence data. It was originally downloaded in fasta format from the National Genomics Data Center webpage and then converted to 2bit by running the faToTwoBit program provided by UCSC. The file <a href="genome.txt">genome.txt</a> lists sequences and their sizes. It was made from the S_chinensis_Apr_2019.2bit sequence file using the twoBitInfo program.
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Both twoBitInfo and faToTwoBit are available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
</p>
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Files with extension .gz were compressed and indexed using bgzip and
tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
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The "bed.gz" format file contains gene models from a GFF-format file downloaded from the National Genomics Data Center webpage for <a href="https://ngdc.cncb.ac.cn/gwh/Assembly/486/show/">Genome Warehouse genome assembly sc1</a>.
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More information about this genome assembly and its gene models can be found in the following publication: <a href="https://doi.org/10.1126/sciadv.aay3240">The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds</a>.
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1	<html>
2	<body>
3	<h1>Simmondsia chinensis (Apr 2019) Jojoba (sc1)</h1>
4	<p>
5	The files listed below are formatted for visualization in the Integrated Genome Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
6	</p>
7	<p>
8	The file named S_chinensis_Apr_2019.2bit contains sequence data. It was originally downloaded in fasta format from the National Genomics Data Center webpage and then converted to 2bit by running the faToTwoBit program provided by UCSC. The file <a href="genome.txt">genome.txt</a> lists sequences and their sizes. It was made from the S_chinensis_Apr_2019.2bit sequence file using the twoBitInfo program.
9	</p>
10	<p>
11	Both twoBitInfo and faToTwoBit are available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
12	</p>
13	<p>
14	Files with extension .gz were compressed and indexed using bgzip and
15	tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
16	</p>
17	<p>
18	The "bed.gz" format file contains gene models from a GFF-format file downloaded from the National Genomics Data Center webpage for <a href="https://ngdc.cncb.ac.cn/gwh/Assembly/486/show/">Genome Warehouse genome assembly sc1</a>.
19	</p>
20	<p>
21	More information about this genome assembly and its gene models can be found in the following publication: <a href="https://doi.org/10.1126/sciadv.aay3240">The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds</a>.
22	</p>
23	</body>
24	</html>