d5b482e55f12f625e0c94de419a58d8a1d746791 dschmelt Thu Mar 11 14:08:56 2021 -0800 Adding links to hgTracks etx. refs #27173 diff --git src/hg/htdocs/goldenPath/help/covidBrowserIntro.html src/hg/htdocs/goldenPath/help/covidBrowserIntro.html index d03951a..0fbbe31 100755 --- src/hg/htdocs/goldenPath/help/covidBrowserIntro.html +++ src/hg/htdocs/goldenPath/help/covidBrowserIntro.html @@ -1,66 +1,69 @@ <!DOCTYPE html> -<!--#set var="TITLE" value="COVID Genome Browser Intro" --> +<!--#set var="TITLE" value="COVID Browser Intro" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Introduction to the SARS-CoV-2 Genome Browser</h1> <div class="row"> <div class="col-sm-6"> <p> The UCSC Genome Browser is an open-source, interactive sequence visualization tool that has been a cornerstone of genomics since we released the first human genome assembly 20 years ago. Cited in more than 37,000 scientific articles and used by thousands of researchers each day; it allows for cross-referencing of research, clinical, -and epidemiology data against reference genomes, including SARS-CoV-2. This data is continuously +and epidemiology data against reference genomes, including +<a href="../../cgi-bin/hgGateway?db=wuhCor1">SARS-CoV-2</a>. This data is continuously updated and added to as new datasets become available. For a more thorough description, please reference our <a href="https://www.nature.com/articles/s41588-020-0700-8" target="_blank"> SARS-CoV-2 Genome Browser Nature Genetics paper</a>. We also post updates and COVID Browser resources to out <a href="../../covid19.html">COVID-19 Browser home page</a>.</p> <p> This guide will go through some of the most important use cases of the SARS-CoV-2 Genome Browser. These topics include:</p> <ul> <li><a href="#nav">Orientation and Navigation</a></li> <li><a href="#genes">Gene Data and Sequence Alignments</a></li> <li><a href="#var">Variation and Immunology data</a></li> <li><a href="#usher">Phylogenetic Contact Tracing using USHER</a></li> <li><a href="#data">Other tools and data downloads</a></li> <li><a href="#support">Support and Collaboration</a></li> </ul> <p> For those who prefer a video explanation, we also have the following tutorial:</p> </div> <div class="col-md-6"> <p> <iframe width="560" height="315" src="https://www.youtube.com/embed/Ee6h0xyZDOM?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe></p> </div> </div> <a name="nav"></a> <h2>Genome Browser Orientation and Navigation</h2> <p> -The standardized reference genome sequence shown is from one of the first isolated cases, known as -<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2" target="_blank">NC_045512v2</a> -or wuhCor1. With more than 80 track datasets across the SARS-CoV-2 reference genome's nearly 30,000 RNA +The standardized reference genome displayed on the +<a href=../../hgTracks?db=wuhCor1">COVID Genome Browser</a> is from one of the first isolated +cases, known as <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2" +target="_blank">NC_045512v2</a> or wuhCor1. With more than 80 track datasets across the +SARS-CoV-2 reference genome's nearly 30,000 RNA bases, navigation is essential to finding the information you want to see. Below is an example -view of the Genome Browser with labeled sections highlighting the navigation, reference sequence, -annotations, and other available track datasets.</p> +view of the SARS-CoV-2 Genome Browser with labeled sections highlighting the navigation, +reference sequence, annotations, and other available track datasets.</p> <p> <b>Navigation controls</b> at the top allow users to move left and right and to zoom. The <b>search box</b> allows users to search for particular features or to move to exact genomic coordinates. The <b>RNA sequence</b> is shown at the top only when the view is sufficiently zoomed in. Annotations are shown for data tracks that have been set to visible in the <b>available tracks</b> section at the bottom. Tracks can be configured with a right-click or by clicking on their name near the bottom of the page.</p> <p class="text-center"> <a href="http://genome.ucsc.edu/s/SARS_CoV2/Figure1"><img class="text-center" src="../../images/covidBrowserIntroNav.png" alt="Labeled orientation to the Genome Browser" width="1200" height="594"></a> <p class="gbsCaption text-center">This is a view of the SARS-CoV-2 Genome Browser (COVID Browser) @@ -111,31 +114,31 @@ conservation tracks available on the SARS-CoV-2 genome. You should be able to see UniProt protein products, regions of interest, and domains all mapped against the SARS-CoV-2 genome. Below those tracks are two different conservation alignments in "squish" and "pack" formats, comparing bat-host and human-host coronavirus sequences with the reference SARS-CoV-2 genome. Interact with this session by clicking on the picture. </p> </p> </div> </div> <a name="var"></a> <h2>Exploring Variation and Immunology Data</h2> <div class="row"> <div class="col-md-5"> <p> -The SARS-CoV-2 Genome Browser displays data on variation within SARS-CoV-2 +The <a href="../../cgi-bin/hgTracks?db=wuhCor1">SARS-CoV-2 Genome Browser</a> displays data on variation within SARS-CoV-2 from UniProt, GenBank, GISAID, Nexstrain, and other providers. These datasets cover global trends in SARS-CoV-2 variation among all available public sequences, with regional descriptions available through clicking into a particular entry. A few of the most notable tracks under the "Variation and Repeats" section are the <a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=sarsCov2PhyloPub">Phylogeny: Public track</a>, which shows a continuously updating phylogenetic tree that clusters similar sequences, with the frequency of each mutation shown by the height of the bar at that particular base. Tools are provided to filter these data to show only well-supported mutation calls, set thresholds for minor-allele frequency, and display data for specific clades.</p> <p> Another track is the spike protein mutations from community annotations, highlighted as amino acid changes with red indicating strong antibody escape in receptor-binding domain (RBD) mutation screens. The Genome Browser has also has the <a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts">Variants of Concern track</a>, which @@ -177,46 +180,49 @@ sequences onto existing phylogenetic trees far faster than previous methods, allowing instantaneous tracing of strains and transmission events. This tool is called <a href="../../cgi-bin/hgPhyloPlace">Ultrafast Sample placement on Existing tRees (UShER)</a> and exists as an interactive web-tool to compare sequences and link to existing public phylogenetic trees. <p class="text-center"> <a href="../../cgi-bin/hgPhyloPlace"><img class="text-center" src="../../images/covidBrowserIntroUShER.png" alt="Example of the UShER phylogeny placement tool" width="1200" height="355"></a> <p class="gbsCaption text-center">After uploading a Fasta file, the tool returns a page with quality metrics such as: number of bases aligned, number of Ns, and number of maximally parsimonious placements along with the lineage and clade of the nearest neighbor. Colored boxes highlight possible quality issues, green meaning this was a high confidence placement.</p> -<h3>SARS-CoV-2 Phylogenic Trees</h3> +<h3>SARS-CoV-2/ COVID Phylogenic Trees</h3> <p> You can view your aligned SARS-CoV-2 sequence genotypes along with their closest known relatives among the 150,000+ public sequences. You can compare among your uploaded samples or trace possible transmission vectors using mutational signatures.</p> + <p class="text-center"> <a href="http://genome.ucsc.edu/s/dschmelt/covidBrowserIntroUShER2"><img class="text-center" src="../../images/covidBrowserIntroUShER2.png" alt="Example of the UShER phylogeny placement tool tree features" width="800" height="427"></a> <p class="gbsCaption text-center">The uploaded sequences are highlighted in blue alongside their most closely aligned public sequences. You can investigate genotypes and relationships between samples.</p> +</p> + <a name="data"></a> -<h2>Other tools and features</h2> +<h2>Other tools, downloads, and features</h2> <h3>Custom Tracks, BLAT, Track Hubs</h3> <p> Along with a suite of data tracks, filters, and visualization options for the SARS-CoV-2 genome, the UCSC Genome Browser offers many additional ways to interface with our data. You can upload your data on the reference genome in <a href="../../FAQ/FAQformat.html">nearly any format</a> with our <a href="../..//cgi-bin/hgCustom">Custom Track tool</a>. If you have unaligned sequence, you can use our <a href="../../cgi-bin/hgBlat">BLAT sequence alignment tool</a> to get coordinates and base-by-base comparison with any reference genome. We also display formatted data as <a href="hgTrackHubHelp.html">Track Hubs</a> and curate a list of user-submitted <a href="../../cgi-bin/hgHubConnect?#publicHubs">Public Track Hubs</a>. </p> <h3>Downloads, Table Browser, JSON API, SQL</h3> <p>