/[genomes]/quickload/D_rerio_Jul_2010/HEADER.md
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Contents of /quickload/D_rerio_Jul_2010/HEADER.md

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Revision 88 - (show annotations)
Tue Jan 15 22:11:30 2019 UTC (18 months, 3 weeks ago) by aloraine
File size: 1179 byte(s)
Add description for new genome versions ce11, chlSab2, C. albicans
1 <html>
2 <body>
3 <h1>Danio rerio (Jul 2010) zebrafish (Zv9/danRer7) 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 Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome
10 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 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
17 </p>
18 <p>
19 The file named D_rerio_Jul_2010.2bit contains sequence data and is from the UCSC Genome
20 Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file
21 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
22 D_rerio_Jul_2010.2bit sequence file using twoBitInfo.
23 </p>
24 <p>
25 Both twoBitInfo and twoBitToFa are
26 available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
27 </p>
28 </body>
29 </html>

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