quickload/A_mellifera_Jan_2005/HEADER.md

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<h1>Apis mellifera (honeybee) Jan 2005 (apiMel2/Baylor College of Medicine HGSC v.Amel_2.0 ) genome assembly</h1>
<p>
The files listed below are formatted for visualization in the Integrated Genome
Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
Bioinformatics Table Browser. Each file is named for its corresponding table in the
UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
this directory for details.
</p>
<p>
Files with extension .gz were compressed and indexed using bgzip and
tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
</p>
<p>
The file named A_mellifera_Jan_2005.2bit contains sequence data and was downloaded from the UCSC Genome
Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
page</a>. To convert a .2bit to fasta, use twoBitToFa. The file
<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from 
A_mellifera_Jan_2005.2bit sequence file using twoBitInfo.
</p>
<p>
Both twoBitInfo and twoBitToFa are
available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
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1	aloraine	12	<html>
2			<body>
3			<h1>Apis mellifera (honeybee) Jan 2005 (apiMel2/Baylor College of Medicine HGSC v.Amel_2.0 ) genome assembly</h1>
4			<p>
5			The files listed below are formatted for visualization in the Integrated Genome
6			Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
7			</p>
8			<p>
9	aloraine	79	Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10	aloraine	12	Bioinformatics Table Browser. Each file is named for its corresponding table in the
11			UCSC Genome database. See the <a href="annots.xml">annots.xml</a> meta-data file in
12			this directory for details.
13			</p>
14			<p>
15			Files with extension .gz were compressed and indexed using bgzip and
16	aloraine	79	tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17	aloraine	12	</p>
18			<p>
19			The file named A_mellifera_Jan_2005.2bit contains sequence data and was downloaded from the UCSC Genome
20			Bioinformatics <a href="http://hgdownload-test.sdsc.edu/downloads.html">downloads
21			page</a>. To convert a .2bit to fasta, use twoBitToFa. The file
22			<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
23			A_mellifera_Jan_2005.2bit sequence file using twoBitInfo.
24			</p>
25			<p>
26			Both twoBitInfo and twoBitToFa are
27			available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
28			</p>
29			</body>
30			</html>