d24afd28f8d2bc57bbb906ba4303b0dabfd7b212
steve
  Wed Apr 1 15:29:44 2015 -0700
Updated docs for danRer10 release; refs #14017

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 <!-- News Section ============================================- -->  
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                  <font size="4"><a name="TOC"></a><b>&nbsp; News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" title="Follow &#64;GenomeBrowser on Twitter" alt="Follow &#64;GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a>
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           <P>
           To receive announcements of new genome 
           assembly releases, new software features, updates and 
           training seminars by email, subscribe to the
           <A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en"
           TARGET=_blank>genome-announce</A> mailing list. Please see our
           <a href="http://genome.ucsc.edu/blog"
           target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more.
           </p>
 
     <!-- start news -->
         <hr>
         <p>
-        <font face="courier" size="3"><b>17 March 2015 - New Visualization Option for RepeatMasker</b></font>
+        <font face="courier" size="3"><b>01 April 2015 - New GRCz10 Zebrafish Assembly Now Available</b></font>
+        <p>
+        The most recent zebrafish assembly -- GRCz10 (UCSC version danRer10, Sep. 2014) -- is now
+        available in the UCSC Genome Browser. This is the first zebrafish release by the
+        <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/zebrafish/"
+         target="_blank">Genome Reference Consortium</a>, who took over the improvement and
+        maintenance of the zebrafish genome assembly.
+        </p>
+
+        <p>
+        The GRCz10 assembly improves upon Zv9 by utilizing optical mapping and additional meiotic
+        mapping to fill gaps with new clone sequence and improve the positioning of assembly
+        components.  This has also been supplemented with a new whole genome shotgun assembly
+        WGS31. The result is an assembly with a sequence length of 1.3 Gb in 26 chromosomes and
+        1,035 scaffolds.  For more details about the GRCz10 assembly, see the
+        <a href="http://www.ncbi.nlm.nih.gov/assembly/210611"
+         target="_blank">GRCz10 assembly page</a> or the official
+        <a href="http://www.ncbi.nlm.nih.gov/news/10-08-2014-zebrafish-grcz10-annotated/"
+         target="_blank">GRCz10 announcement</a>.
+        </p>
+
+        <p>
+        The danRer10 sequence and annotation data can be downloaded from the UCSC Genome Browser
+        <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/">FTP server</a> or
+        <a href="http://hgdownload.cse.ucsc.edu/downloads.html#zebrafish">downloads</a> page.
+        </p>
+
+        <p>
+        We'd like to thank the Genome Reference Consortium for providing this assembly. The UCSC
+        zebrafish Genome Browser was produced by Hiram Clawson, Brian Raney and Steve Heitner. See the
+        <a href="../goldenPath/credits.html#zebrafish_credits">credits</a> page for a detailed list
+        of the organizations and individuals who contributed to this release.
+        </p>
+
+        <hr>
+        <p>
+        <font face="courier" size="3"><b>20 March 2015 - New Visualization Option for RepeatMasker</b></font>
         <p>
 	We are excited to announce the release of the new RepeatMasker Visualization track for the
 	hg38 and mm10 assemblies. This new RepeatMasker track displays detailed information that
 	includes the amount of unaligned repeat sequence and lines joining repeat fragments.
 	Additionally, repeats are now colored based on their repeat class. This new RepeatMasker
 	track incorporates a new details page that includes the detailed RepeatMasker output and
 	the raw alignment used to generate the final repeat annotation. You can read more about
 	this track on the description page for either
 	<a href="../cgi-bin/hgTrackUi?db=hg38&g=rmskJoinedBaseline">hg38</a> or
 	<a href="../cgi-bin/hgTrackUi?db=mm10&g=rmskJoinedBaseline">mm10</a>.
 	</p>
 
 	<p>
 	This track is the result of a collaboration between the
 	<a href="http://www.systemsbiology.org/" target="_blank">Institute for Systems Biology</a>
 	and the UCSC Genome Browser. We would like to thank Robert Hubley, Arian Smit, Hiram
 	Clawson, and Matthew Speir for their efforts in creating this track.
 	</p>
 
         <hr>
-        <p>
-        <font face="courier" size="3"><b>03 March 2015 - Use UDR for Quick Sizable Downloads</b></font>
-        <p>
-        The UCSC Genome Browser is pleased to share a download protocol to use when downloading
-        large sets of files from our download servers: <b>UDR (UDT Enabled Rsync)</b>. UDR utilizes rsync
-        as the transport mechanism, but sends the data over the UDT protocol, which enables huge
-        amounts of data to be downloaded efficiently over long distances.</p>
-        <p>
-        Protocols like http, ftp and rsync can have a problem in that the further
-        away the download source is from the user, the slower the speed becomes. Protocols like UDT/UDR
-        allow for many UDP packets to be sent in batch, thus allowing for much higher transmit speeds
-        over long distances. UDR will be especially useful for users who are downloading from places
-        that are far away from California. The US East Coast and the international community will likely
-        see much higher download speeds by using UDR rather than rsync, http or ftp.
-        <a href="goldenPath/newsarch.html#030315">Read more</a>.
-        <hr>
 
         <!-- start archives -->
 <!--
-        <font face="courier" size="3"><b>17 March 2015 - New Visualization Option for RepeatMasker</b>: </font>
+        <font face="courier" size="3"><b>01 April 2015 - New GRCz10 Zebrafish Assembly Now Available</b>: </font>
+        The most recent zebrafish assembly -- GRCz10 (UCSC version danRer10, Sep. 2014) -- is now
+        available in the UCSC Genome Browser.
+        <a href="goldenPath/newsarch.html#040115">Read more</a>.
+
+        <font face="courier" size="3"><b>20 March 2015 - New Visualization Option for RepeatMasker</b>: </font>
 	We are excited to announce the release of the new RepeatMasker Visualization track for the
 	hg38 and mm10 assemblies.
         <a href="goldenPath/newsarch.html#032015">Read more</a>.
+-->
 
+        <p>
 	<font face="courier" size="3"><b>03 March 2015 - Use UDR for Quick Sizable Downloads</b>: </font>
         The UCSC Genome Browser is pleased to share a download protocol to use when downloading
         large sets of files from our download servers: <b>UDR (UDT Enabled Rsync)</b>. UDR utilizes rsync
         as the transport mechanism, but sends the data over the UDT protocol, which enables huge
         amounts of data to be downloaded efficiently over long distances.
         <a href="goldenPath/newsarch.html#030315">Read more</a>.
---> 
 
         <p>
         <font face="courier" size="3"><b>26 February 2015 - New Training Video!</b></font>
         View it now on our
         <a href="http://bit.ly/genomebrowserYoutube" target="_blank">YouTube channel</a>.
         <a href="goldenPath/newsarch.html#022615">Read more</a>.
-	<p>
-        <font face="courier" size="3"><b>12 February 2015 - Blat Your Assembly Hub</b>: </font>
-        Assembly data hubs, track hubs that allow researchers to annotate genomes that are
-        not in the UCSC Genome Browser, can now use blat to quickly find DNA and protein
-        sequences in their unique assemblies.
-        <a href="goldenPath/newsarch.html#021215">Read more</a>.
 
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