008dba8f4169e0de018a6e102caf07193e4ad33c lrnassar Thu Jul 16 14:56:03 2026 -0700 Point hs1 linkouts in Long-read SVs announcement to hgTracks without g= (hs1 served as file/hub assembly). refs #36258 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index f60204f8770..39e6430dd7a 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -282,31 +282,31 @@ improving the expansive track hubs for ENCODE4 and for iterating with us to bring them to the browser as native tracks. We also thank the ENCODE Consortium, the ENCODE production laboratories, and the ENCODE Data Coordination Center for generating and processing the underlying experiments, and Gerardo Perez, Brian Raney, Max Haeussler, and Lou Nassar for building and reviewing these tracks. </p> --> <a name="071626"></a> <h2>Jul. 16, 2026 Long-read Structural Variants tracks for human (hg38 and hs1)</h2> <p> We are excited to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&g=longReadVariants&position=default" target="_blank"><b>Long-read Structural Variants</b></a> container track on the human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&g=longReadVariants&position=default" target="_blank">GRCh38/hg38</a> and -<a href="/cgi-bin/hgTrackUi?db=hs1&g=longReadVariants&position=default" target="_blank">T2T-CHM13/hs1</a>. +<a href="/cgi-bin/hgTracks?db=hs1&position=default" target="_blank">T2T-CHM13/hs1</a>. The container track brings together structural variant (SV) callsets from 14 long-read sequencing studies worldwide into a single place where you can compare large genomic rearrangements (deletions, insertions, duplications, inversions, and complex events) across populations, cohorts, and calling strategies. Long-read technologies span repetitive regions and resolve complex loci that are difficult to detect with short reads, giving more precise breakpoints and better sensitivity for large variants. </p> <p> At the center of the container track is an <a href="/cgi-bin/hgTrackUi?db=hg38&g=lrSvAll&position=default" target="_blank"><b>All long-read SVs merged</b></a> track that unifies every source callset on identical position, type, and length into roughly 2.3 million distinct SV sites, each carrying per-database allele counts so you can see at a glance how many studies support a given variant and at what frequency. This merged track is the best place to start: we @@ -350,31 +350,31 @@ </p> <table class="stdTbl"> <tr><th>Region / theme</th><th>Contributing studies</th></tr> <tr><td>East Asia</td><td>Han Chinese 945, ToMMo Japan, Chinese Pangenome Consortium</td></tr> <tr><td>1000 Genomes (global)</td><td>1KG ONT 100 (Gustafson), 1KG ONT Vienna (1,019)</td></tr> <tr><td>Americas</td><td>All of Us, GA4K (pediatric rare disease), SVatalog (cystic fibrosis)</td></tr> <tr><td>Europe</td><td>deCODE (Iceland)</td></tr> <tr><td>Middle East</td><td>Arab Pangenome Reference</td></tr> <tr><td>Global reference & pangenome callsets</td><td>CoLoRSdb, HPRC v2.1, HGSVC2, HGSVC3</td></tr> </table> <p> Six of these datasets (CoLoRSdb, 1KG ONT Vienna, HGSVC3, HPRC v2.1, Arab Pangenome Reference, and the Chinese Pangenome Consortium) are also released on the -<a href="/cgi-bin/hgTrackUi?db=hs1&g=longReadVariants&position=default" target="_blank">T2T-CHM13/hs1</a> +<a href="/cgi-bin/hgTracks?db=hs1&position=default" target="_blank">T2T-CHM13/hs1</a> assembly in native coordinates. </p> <p> License restrictions on some sources limit redistribution; see the track description page for per-study details. </p> <p> We plan to keep adding long-read SV callsets as more become available. If you are involved with a project that publishes long-read structural variants and would like to contribute, please <a href="/contacts.html" target="_blank">reach out</a>. </p> <p>