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add resources page
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@hdashnow
hdashnow committed May 4, 2024
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<!DOCTYPE html>
<html>
<head>
<!-- Standard Meta -->
<meta charset="utf-8">

<!-- Site Properties -->
<title>STRchive</title>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/semantic-ui/2.2.7/semantic.min.css">


<style type="text/css">

.hidden.menu {
display: none;
}

.masthead.segment {
min-height: 700px;
padding: 1em 0em;
}
.masthead .logo.item img {
margin-right: 1em;
}
.masthead .ui.menu .ui.button {
margin-left: 0.5em;
}
.masthead h1.ui.header {
margin-top: 3em;
margin-bottom: 0em;
font-size: 4em;
font-weight: normal;
}
.masthead h2 {
font-size: 1.7em;
font-weight: normal;
}

.ui.vertical.stripe {
padding: 8em 0em;
}
.ui.vertical.stripe h3 {
font-size: 2em;
}
.ui.vertical.stripe .button + h3,
.ui.vertical.stripe p + h3 {
margin-top: 3em;
}
.ui.vertical.stripe .floated.image {
clear: both;
}
.ui.vertical.stripe p {
font-size: 1.33em;
}
.ui.vertical.stripe .horizontal.divider {
margin: 3em 0em;
}

.quote.stripe.segment {
padding: 0em;
}
.quote.stripe.segment .grid .column {
padding-top: 5em;
padding-bottom: 5em;
}

.footer.segment {
padding: 5em 0em;
}

.secondary.pointing.menu .toc.item {
display: none;
}

@media only screen and (max-width: 700px) {
.ui.fixed.menu {
display: none !important;
}
.secondary.pointing.menu .item,
.secondary.pointing.menu .menu {
display: none;
}
.secondary.pointing.menu .toc.item {
display: block;
}
.masthead.segment {
min-height: 350px;
}
.masthead h1.ui.header {
font-size: 2em;
margin-top: 1.5em;
}
.masthead h2 {
margin-top: 0.5em;
font-size: 1.5em;
}
}


</style>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
<script>
$(document)
.ready(function() {

// fix menu when passed
$('.masthead')
.visibility({
once: false,
onBottomPassed: function() {
$('.fixed.menu').transition('fade in');
},
onBottomPassedReverse: function() {
$('.fixed.menu').transition('fade out');
}
})
;

// create sidebar and attach to menu open
$('.ui.sidebar')
.sidebar('attach events', '.toc.item')
;

})
;
</script>
</head>
<body>

<!-- Header -->
<div class="pusher">
<div class="ui inverted vertical center aligned segment">

<div class="ui container">
<div class="ui large secondary inverted pointing menu">
<a class="toc item">
<i class="sidebar icon"></i>
</a>
<a class="item" href="index.html">Home</a>
<a class="item" href="about.html">About</a>
<a class="item" href="/database/index.html">STR Database</a>
<a class="item" href="plots.html">Plots</a>
<a class="active item" href="resources.html">Resources</a>
<a class="item" href="contribute.html">Contribute</a>
<div class="right item">
<a class="ui inverted button" href="index.html">STRchive</a>
<a class="ui icon inverted button" href="https://github.com/hdashnow/STRchive">
<i class="github icon"></i>
</a>
</div>
</div>
</div>
</div>
</div>

<!-- Page Contents -->
<!---- [ ] Genotyping methods
- [ ] Differences between TR locus definitions and why
- [ ] Genome-wide TR loci resources
Both versions of the Palladium? TRF default and 7M?
Adotto - may overestimate size.
-->


<div class="ui vertical stripe segment">
<div class="ui middle aligned stackable grid container">
<div class="row">
<div class="eight wide column">

<h3 class="ui header">Computational methods</h3>
<p>
A selection of computational methods that we have either developed or
used in our research. For a more comprehensive review of methods, see
<a href="https://doi.org/10.1038/s41576-024-00692-3">
Tanudisastro et al. (2024)</a>.
</p>
<p>
Short-read genotyping methods
<li><a href="https://github.com/Illumina/ExpansionHunter">ExpansionHunter</a></li>
<li><a href="https://github.com/gymrek-lab/HipSTR">HipSTR</a></li>
<li><a href="https://github.com/gymreklab/gangstr">gangSTR</a></li>
</p>
<p>
Short-read novel locus detection methods
<li><a href="https://github.com/quinlan-lab/STRling">STRling</a></li>
<li><a href="https://github.com/Illumina/ExpansionHunterDenovo">ExpansionHunter Denovo</a></li>
</p>
<p>
Long-read genotyping methods
<li><a href="https://github.com/PacificBiosciences/trgt">TRGT</a></li>
<li><a href="https://github.com/PacificBiosciences/trgt-denovo">TRGT-denovo</a></li>
</p>


</div>
<div class="six wide right floated column">
<h3 class="ui header">Tandem repeat catalogs</h3>
<p>
<li><a href="https://github.com/broadinstitute/str-analysis/tree/main/str_analysis/variant_catalogs">gnomAD disease loci: ExpansionHunter format</a></li>
<li><a href="https://github.com/Illumina/RepeatCatalogs">174,293 polymorphic STRs: ExpansionHunter format</a>
<li><a href="https://github.com/PacificBiosciences/trgt/blob/main/repeats/repeat_catalog.hg38.bed">174,293 polymorphic STRs: TRGT format</a>
</p>

<h3 class="ui header">Databases</h3>
<p>
<li><a href="https://gnomad.broadinstitute.org/short-tandem-repeats">gnomAD: Tandem Repeats</a></li>
<li><a href="https://stripy.org/">STRipy</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/books/NBK535148/">GeneReviews: Tandem Repeat Disorders</a></li>
<li><a href="https://omim.org/">OMIM</a>
</p>

</div>
</div>
<div class="row">
<!-- <div class="center aligned column">
<a class="ui huge button">Check Them Out</a>
</div> -->
</div>
</div>
</div>




<div class="ui vertical stripe segment">
<div class="ui text container">

<h3 class="ui header">Why do repeat locus definitions differ between resources?</h3>
<p>
There are often multiple ways to define a given repeat locus. For example,
defining a locus as a stretch of perfectly repeting motifs tends to result in
a narrower locus than strategies allowing for interruptions. In coding regions the
locus boundary might be chosen to align with the reading frame.
</p>
<p>
There are often multiple "correct" ways to define a given repeat locus, however
careful consideration must be made to the downstream uses of the data.
In particular, genotyping accuracy can be affected by the choice of locus definition.
</p>
<p>
The loci in STRchive were defined to be broader, allowing for interruptions, and
with consideration to the biological context and clinical utility of the locus.
This strategy increases the chance that the locus will overlap with a relevant
variant call when STRchive is used to annotate a VCF file. It is also the preferred
approach to defining loci for improved genotyping accuracy with
<a href="https://github.com/PacificBiosciences/trgt">TRGT</a>.
In contrast,
<a href="https://github.com/Illumina/ExpansionHunter">ExpansionHunter</a>
tends to perform better with narrower loci that
exclude repeat interruptions. For this reason, repeat definitions used in
<a href="https://gnomad.broadinstitute.org/short-tandem-repeats">gnomAD</a>
tend to be narrower than those used in STRchive.
</p>

</div>
</div>


</div>

<!-- Footer -->
<div class="ui inverted vertical footer segment">
<div class="ui container">
<div class="ui stackable inverted divided equal height stackable grid">
<div class="three wide column">
<a class="item" href="about.html">
<h4 class="ui inverted header">About</h4>
</a>
<div class="ui inverted link list">
<a class="item" href="https://github.com/hdashnow/STRchive/issues">Contact Us</a>
</div>
</div>
<div class="three wide column">
<a class="item" href="contribute.html">
<h4 class="ui inverted header">Contribute</h4>
</a>
<div class="ui inverted link list">
<a class="item" href="contribute.html">How To Contribute</a>
</div>
</div>
<div class="ten wide column">
<h4 class="ui inverted header">Research use only</h4>
<p>The content on and linked from this website
does not constitute and shall not be construed as constituting medical or legal advice of any kind whatsoever,
nor is it a substitute for professional medical advice, diagnosis and treatment.
</p>
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/">
<img class="ui tiny image right floated" alt="Creative Commons License"
style="border:0.5px solid silver;"
src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
<span xmlns:dct="http://purl.org/dc/terms/"
href="http://purl.org/dc/dcmitype/Dataset" property="dct:title"
rel="dct:type">STRchive</span> is licensed under a
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/">
Creative Commons Attribution 4.0 International License</a>.
</div>
</div>
</div>
</div>


</body>

</html>

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