6cdc3f8d72e6f83675f24cf18df1dbcfb97c7743 gperez2 Tue Oct 19 12:34:30 2021 -0700 Updating news for the hg38 patch 13 announcement, refs #25091 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index c2b725e..06bd0f0 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,75 @@ <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> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="101221"></a> +<h2>Oct. 18, 2021 Addition of GRCh38 patch 13 sequences to hg38</h2> +<p> +We are pleased to announce the addition of GRCh38 patch release 13 to the +<a href="../../cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches +since its release in 2013. The GRC patch releases do not change any previously existing +sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond +to specific regions of the main chromosome sequences. For most users, the patches are unlikely +to make a difference and may complicate the analysis as they introduce more duplication.</p> + +<p> +More information on how patch sequences are incorporated can be found on the +<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +The blog post contains details about the new +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" +target="_blank">/latest</a>, +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/" +target="_blank">/initial</a>, and +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p13/" target="_blank">/p13</a> +download directories on the downloads server. With the addition of new sequences to hg38, we can +expect to see BLAT return more matches to the genome.</p> + +<ul> + <li> + The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455 + sequences, 261 alternate sequences, and no fix sequences. It is the same as the + parent download directory. This is probably the best genome file for aligners and most analysis + tasks, a version called "analysisSet" for the human genome. + </li> + <li> + The <b>p13/</b> subdirectory contains files for GRCh38.p13 (patch release 13). It has 640 sequences + including alternate and fix sequences. + </li> + <li> + The <b>latest/</b> symbolic link points to the subdirectory for the most recent patch version. + </li> +</ul> + +<p> +We would like to thank the <a href="https://www.ncbi.nlm.nih.gov/grc" target="_blank">Genome +Research Consortium</a> for creating the patches for hg38. We would also like to thank Galt Barber, +Jairo Navarro, and Gerardo Perez at UCSC for implementing and testing the latest patch to the +hg38 genome.</p> + + <a name="101521"></a> <h2>Oct. 15, 2021</h2> <p>The UCSC Genom Browser is proud to share our latest update to the SARS-CoV-2 browser, the updated <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> Variants of Concern (VOC) track</a>. This data track includes amino acid and nucleotide annotations for 10 different COVID variants, including the Delta and Mu variants, mapped along the SARS-CoV-2 reference genome. These variants are <a href="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/" target="_blank">classified by the WHO</a> into several categories: Variants of Concern (VOC), Variants of Interest (VOI), and Variants under Investigation (VUM). These tracks help provide a more clear understanding of the mutations that comprise each named variant. This track's items also include links to <a target="_blank" href="https://outbreak.info"> Outbreak.info</a>, providing geographic distibutions for each variant.