23157e10e700d6c8e8d9a069d30934dd8d34de9e lrnassar Wed Jun 24 15:13:42 2020 -0700 Release announcement for VGP update refs #25555 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2949c9c..b98633a 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,98 @@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="062520"></a> +<h2>Jun. 25, 2020 Vertebrate Genomes Project assembly hub update</h2> +<p> +We are proud to announce our first major update to the <a href="https://hgdownload.soe.ucsc.edu/hubs/VGP/" +target="_blank">Vertebrate Genomes Project assembly hub</a>. This is a follow up to our +<a href="#082819">initial release</a>, and expands the hub to 168 assemblies.</p> +<p> +With this update, we have created three additional hubs in addition to the main hub:</p> + +<ul> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/index.html"> +<b>Primary assembly (72)</b></a> - Main hub which contains the primary +assemblies for each of the organisms.</li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAlt.html"> +<b>Alternate/haplotype (68)</b></a> - Secondary hub which contains alternate +haplotype assemblies for a subset of the organisms in the primary hub.</li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrio.html"> +<b>Trio mat/pat (17)</b></a> - Secondary hub which contains trio assemblies (child, maternal, +paternal) for a subset of the organisms in the primary hub.</li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacy.html"> +<b>Legacy/superseded (11)</b></a> - Hub containing previous assemblies that have since been updated.</li> +</ul> + +<p> +As with the previous release, all assemblies are built with a minimum set of data tracks including +gene annotations, CpG islands, GC content, and repeat masking. <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics</a> and +<a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/trackData.html"> +track statistics</a> are also available for all hubs. Links to the different pages are included +below:</p> + +<p> +<table border='1'><thead> +<tr><th colspan=5 style='text-align:center;'>Available VGP assemblies</th></tr> +<tr><th>Index pages: </th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/index.html'>primary assembly</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAlt.html'>alternate/haplotype</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrio.html'>trio mat/pat</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacy.html'>legacy/superseded</a></th> +</tr><tr> +<th>Assembly statistics: </th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStats.html'>primary assembly</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAltStats.html'>alternate/haplotype</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrioStats.html'>trio mat/pat</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacyStats.html'>legacy/superseded</a></th> +</tr><tr> +<th>Track statistics: </th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/trackData.html'>primary assembly</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAltData.html'>alternate/haplotype</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrioData.html'>trio mat/pat</a></th> +<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacyData.html'>legacy/superseded</a></th> +</tr><tr> +</tr></thead> +</table></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, e.g. +<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 these assembly hubs.</p> + <a name="061920"></a> <h2>Jun. 19, 2020 Updated Self Chain track for human (GRCh38/hg38)</h2> <p> We have updated the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr16&g=chainSelf"> Self Chain</a> track for the human GRCh38/hg38 assembly. The Self Chain track shows alignments of the human genome with itself, using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. After filtering out the alignments produced when identical locations of the genome map to one another (e.g. chrN mapping to chrN), the remaining alignments point out areas of duplication within the human genome.</p> <p> The updated track now includes 33,039,051 chains, and should provide improved sensitivity for pseudogenes and other homologous regions. For more information, see the track <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr16&g=chainSelf">description page</a>.</p> <p>