eab458fb9e14a1e11f3f0f8a8e1cfe5e3215b48e
lrnassar
  Wed Aug 21 15:40:35 2019 -0700
Release announcement for VGP reds #23734

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 <!-- ============= 2019 archived news ============= -->
 <a name="2019"></a>
 
+<a name="082619"></a>
+<h2>Aug. 26, 2019 &nbsp;&nbsp; Vertebrate Genomes Project assembly hub</h2>
+
+<p>
+The UCSC Genome Browser is proud to announce its <a href="https://hgdownload.soe.ucsc.edu/hubs/VGP/" 
+target="_blank">Vertebrate Genomes Project assembly hub</a>. The <a 
+href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genomes Project (VGP)</a> 
+aims to generate near error-free reference genome assemblies of all 70,000 extant 
+vertebrate species.</p>
+
+<p>
+As of now, the <a href="https://hgdownload.soe.ucsc.edu/hubs/VGP/" 
+target="_blank">VGP assembly hub</a> includes 24 vertebrate assemblies. See our <a 
+href="https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStatsVGP.html" 
+target="_blank">assembly statistics page</a> for specific information (gap counts, 
+masking percent, genome size, etc.) on each individual assembly. All assemblies have a 
+combination of Genome Browser generated data tracks, as well as external data. These include:</p>
+<ul>
+  <li>Augustus gene predictions on all assemblies, as well as imported NCBI gene predictions 
+when available.</li>
+  <li>A RefSeq mRNAs track which is generated in-house, mapping RefSeq mRNAs from various other 
+organisms to each individual assembly. This track includes origin mRNA species and gene names, 
+which may help to identify genes on the less annotated assemblies.</li>
+  <li>CpG island and GC percent tracks.</li>
+  <li>Repeat masking tracks by both RepeatMasker and WindowMasker + SDust.</li></ul>
+<p>
+These tracks also include individual track description pages with a summary of their contents 
+or results where applicable. Such as a summary of all RepeatMasker elements found in the 
+<a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=hub_1489433_GCA_007474595.1_mLynCan4_v1.p&g=hub_1489433_repeatMasker" 
+target="_blank">Canada lynx</a> or gene count and genome coverage of NCBI genes for the 
+<a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=hub_1489433_GCF_004115215.1_mOrnAna1.p.v1&g=hub_1489433_ncbiGene" 
+target="_blank">platypus</a>.</p>
+
+<p>
+All data are available from the UCSC download servers. For information on how to download 
+specific assembly data, refer to the assembly gateway page once the hub is connected. Here 
+is an example of the gateway page for the 
+<a href="../../cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004115265.2_mRhiFer1_v1.p" 
+target="_blank">greater horseshoe bat</a>. This page also includes information on starting 
+a local BLAT server for the assembly.</p>
+
+<p>
+We would like to thank the <a href="https://vertebrategenomesproject.org/" 
+target="_blank">Vertebrate Genomes Project</a> and the <a href="https://genome10k.soe.ucsc.edu/" 
+target="_blank">Genome 10k Project</a> for their sequencing efforts and making these genomes 
+available. We would also like to thank Hiram Clawson and Luis Nassar from the Genome Browser team 
+for the development and release of this assembly hub.</p>
+
 <a name="073119"></a>
 <h2>Jul. 31, 2019 &nbsp;&nbsp; New Genome Browser: Horse, equCab3 (<em>Equus caballus</em>)</h2>
 <p>
 A genome browser is now available for the <em>Equus caballus</em> assembly released in Jan. 2018 by the
 <a href="https://louisville.edu/medicine/" target="_blank"> University of Louisville</a> (EquCab3.0).
 <h3>About the assembly:</h3>
 <ul>
   <li><b>UCSC Genome Browser assembly ID:</b>  <a href="../../cgi-bin/hgGateway?db=equCab3" 
   target="_blank">equCab3</a></li>
   <li><b>Sequencing/Assembly provider ID:</b> <a href="https://louisville.edu/medicine/">
 University of Louisville</a></li>
   <li><b>Assembly date:</b> Jan. 2018</li>
   <li><b>Accession ID:</b> GCF_002863925.1</li>
   <li><b>NCBI Genome ID:</b> <a href="https://www.ncbi.nlm.nih.gov/genome/145"
 target="_blank">145</a> (<em>Equus caballus</em>)</li>