8ae5db39951014aa1bb2b6fc062aa8263fd1fc91 lrnassar Mon May 25 14:52:06 2020 -0700 Announcing refseq vertebrate assembly hubs refs #23891 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 95424bd..75fc2f6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,83 @@ <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="052620"></a> +<h2>May 26, 2020 NCBI RefSeq assembly hubs </h2> +<p> +We are pleased to announce new NCBI RefSeq assembly hubs for vertebrate genomes. Currently these +hubs contain 295 assemblies, encompassing most RefSeq vertebrate genomes.</p> +<p> +All assemblies contain multiple gene models including NCBI RefSeq annotations, and Ensembl gene +predictions where available. Additional tracks include repeat masking and simple repeat data. +A complete list of available tracks for each assembly can be found in the respective track +statistics page.</p> +<p> +The assemblies are divided into 5 categories, see the assembly statistics link below for a +complete list of available genomes in each hub. Assembly statistics such as genome size, +gaps, and masking are also available for each genome. Lastly, track statistics are also available +displaying all available tracks for each assembly, as well as their genomic coverage.</p><br> + +<ul> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/index.html"> +</b>Primates</b></a> - <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/primates/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/trackData.html"> +Track statistics</a></li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/index.html"> +</b>Mammals</b></a> - <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/mammals/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/trackData.html"> +Track statistics</a></li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/index.html"> +</b>Birds</b></a> - <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/birds/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/trackData.html"> +Track statistics</a></li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/index.html"> +</b>Fish</b></a> - <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/fish/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/trackData.html"> +Track statistics</a></li> +<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/index.html"> +</b>Other vertebrates</b></a> - <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/trackData.html"> +Track statistics</a></li> +</ul> + +<p> +These assemblies can be found on our list of <a target="_blank" href="/cgi-bin/hgHubConnect"> +Public Hubs</a>, or by searching for a species by NCBI accession or name directly from the +<a target="_blank" href="/cgi-bin/hgGateway">Gateway page</a>.</p> +<p> +We would like to thank NCBI RefSeq for making these data available. +We would also like to thank Hiram Clawson and Lou Nassar for the +development and release of these hubs.</p> + <a name="051220"></a> <h2>May 12, 2020 New video: Coronavirus Browser SARS CoV-2 </h2> <p> We are pleased to announce the release of a <a href = "https://www.youtube.com/watch?v=Ee6h0xyZDOM&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target = _blank>new video</a> on our <a href = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target = _blank>YouTube channel</a>, designed to help make the Browser more accessible to those not usually using the Genome Browser, especially virologists and molecular biologists developing assays and vaccines. The video highlights many features that regular Browser users may already know, but in the context of SARS-CoV-2 genome assembly. The Browser coronavirus tour highlights RT-PCR data, UniProt , crowd-sourced data, T-cell Reactive epitopes and comparative genomics data for viral isolates from around the world and those @@ -781,31 +834,31 @@ href="https://www.ncbi.nlm.nih.gov/refseq/MANE/">MANE project</a>, however, RefSeq Select transcripts that have a 100% identical match to a transcript in the Ensembl annotation are given the MANE Select designation. In this way, MANE Select is a subset of RefSeq Select. It should be noted, however, that there are cases where RefSeq Select transcripts are replaced when a different MANE Select transcript is chosen. Once the MANE project is complete, RefSeq Select and MANE Select for human should be nearly the same.</p> <p> In summary, this track provides a functional canonical gene set until the MANE set is complete. More information on this track and data can be found in the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr1&g=refSeqComposite">track description page</a>, NCBI's <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">RefSeq Select page</a>, and the <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/MANE/">MANE page</a>.</p> <p> We would like to thank NCBI for releasing the RefSeq Select data, as well as the NCBI and -Ensembl-GENCODE collaboration for MANE. We would also like to thank Max Haussler and Lou +Ensembl-GENCODE collaboration for MANE. We would also like to thank Max Haeussler and Lou Nassar for the development and release of these tracks.</p> <a name="021120"></a> <h2>Feb. 11, 2020 New GENCODE gene tracks: Human V33 (hg19/hg38) - Mouse M24 (mm10)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="http://www.ensembl.info/2019/10/17/whats-coming-up-in-ensembl-release-99/" target="_blank">Ensembl 99</a>, for three assemblies: <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV33lift37">hg19/GRCh37</a>, <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38c=chr1&g=wgEncodeGencodeV33">hg38/GRCh38</a>, and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm10&c=chr12&g=wgEncodeGencodeVM24">mm10/GRCm38</a>. For human, the GENCODE V33 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following tracks:</p>