f75874a85e09a19a652ca8c06cd72be5fba5482f angie Thu Nov 12 08:59:08 2020 -0800 Added section about hgPhyloPlace/UShER to CoViD-19 landing page. refs #26516 diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index aff5194..75ca004 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -93,30 +93,79 @@ target="_blank">COVID-19 Airways
  • COVID-19 and Influenza Immunophenotyping
  • COVID-19 Cell Atlas
  • COVID-19 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs)
  • HCA-LungMAP COVID-19 Integrated Analysis

    Other Lung datasets in the Cell Browser +

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    UShER for real-time genomic contact tracing

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    + UShER logo + In addition to the Genome Browser, we offer a + web interface to + Ultrafast Sample placement + on Existing tRees (UShER) + (Turakhia et al.), + a tool for identifying the relationships among a user's newly sequenced viral genomes + and all known SARS-CoV-2 virus genomes. UShER identifies relationships between viral + genomes by adding them to an existing phylogenetic tree of similar sequences that + visually depicts the evolutionary relationships among the genome sequences. + This approach empowers "genomic contact tracing". + That is, UShER tells you whether virus genomes are closely related and therefore + possibly from the same source, or if they are distantly related and the infections + come from distinct sources. + When newly sequenced virus genomes are added to a comprehensive tree of previously + sequenced genomes, contact tracers are often able to determine where in the world + those genomes came from. + UShER is the only available method that can do this in "real time". + Our tool places genomes onto a comprehensive global phylogeny of more than 80,000 + virus genomes in less than one second. +

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    + + Example output of UShER + +
    + Example UShER results displayed using + Nextstrain. + Sequences representing a hypothetical outbreak are yellow; + previously sampled sequences are blue. Branches are labeled + by nucleotide mutations.
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