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deploy: def5a19
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shiltemann committed Nov 27, 2023
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12 changes: 6 additions & 6 deletions 404.html
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console.log("Sentry: opt-in");
Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@98e1a6aedea81f92ce802571fef5d1f900f68f46",
release: "galaxy-training-network@def5a1967ee4b3dfe2d49aa3c15eef271d572f3b",
integrations: [new Sentry.BrowserTracing(), new Sentry.Replay()],
sampleRate: 0.1,
tracesSampleRate: 0.1,
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<link rel="preload" href="/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>

<link rel="preload" href="/training-material/assets/css/main.css?v=3" as="style">
<link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1701102786' as='script'>
<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1701102786' as='script'>
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<link rel="stylesheet" href="/training-material/assets/css/main.css?v=3">
<link rel="manifest" href="/training-material/manifest.json">
<meta name="theme-color" content="#2c3143"/>
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</head>
<body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
<script src='/training-material/assets/js/bundle.f1f2de89.js?v=1701102786'></script>
<script src='/training-material/assets/js/bundle.f1f2de89.js?v=1701105684'></script>
<header>
<nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
<div class="container">
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The GTN infrastructure is licensed under <a rel="license" href="https://github.com/galaxyproject/training-material/blob/main/LICENSE.md">MIT</a>
</p>
<p>
Revision <a href="https://github.com/galaxyproject/training-material/commit/98e1a6aedea81f92ce802571fef5d1f900f68f46">98e1a6a</a>, built with Jekyll (4.3.2 | production)
Revision <a href="https://github.com/galaxyproject/training-material/commit/def5a1967ee4b3dfe2d49aa3c15eef271d572f3b">def5a19</a>, built with Jekyll (4.3.2 | production)
</p>
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<div class="col-sm-6" style="text-align: right">
Expand All @@ -258,7 +258,7 @@ <h2 id="we-cant-seem-to-find-the-page-youre-looking-for">We can’t seem to find
</footer>


<script src='/training-material/assets/js/bundle.03aefefa.js?v=1701102786'></script>
<script src='/training-material/assets/js/bundle.03aefefa.js?v=1701105684'></script>

</body>
</html>
12 changes: 6 additions & 6 deletions accessibility.html
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console.log("Sentry: opt-in");
Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@98e1a6aedea81f92ce802571fef5d1f900f68f46",
release: "galaxy-training-network@def5a1967ee4b3dfe2d49aa3c15eef271d572f3b",
integrations: [new Sentry.BrowserTracing(), new Sentry.Replay()],
sampleRate: 0.1,
tracesSampleRate: 0.1,
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<link rel="preload" href="/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>

<link rel="preload" href="/training-material/assets/css/main.css?v=3" as="style">
<link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1701102786' as='script'>
<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1701102786' as='script'>
<link rel='preload' href='/training-material/assets/js/bundle.f1f2de89.js?v=1701105684' as='script'>
<link rel='preload' href='/training-material/assets/js/bundle.03aefefa.js?v=1701105684' as='script'>
<link rel="stylesheet" href="/training-material/assets/css/main.css?v=3">
<link rel="manifest" href="/training-material/manifest.json">
<meta name="theme-color" content="#2c3143"/>
Expand All @@ -83,7 +83,7 @@

</head>
<body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
<script src='/training-material/assets/js/bundle.f1f2de89.js?v=1701102786'></script>
<script src='/training-material/assets/js/bundle.f1f2de89.js?v=1701105684'></script>
<header>
<nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
<div class="container">
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The GTN infrastructure is licensed under <a rel="license" href="https://github.com/galaxyproject/training-material/blob/main/LICENSE.md">MIT</a>
</p>
<p>
Revision <a href="https://github.com/galaxyproject/training-material/commit/98e1a6aedea81f92ce802571fef5d1f900f68f46">98e1a6a</a>, built with Jekyll (4.3.2 | production)
Revision <a href="https://github.com/galaxyproject/training-material/commit/def5a1967ee4b3dfe2d49aa3c15eef271d572f3b">def5a19</a>, built with Jekyll (4.3.2 | production)
</p>
</div>
<div class="col-sm-6" style="text-align: right">
Expand All @@ -308,7 +308,7 @@ <h3 id="additional-features">Additional Features</h3>
</footer>


<script src='/training-material/assets/js/bundle.03aefefa.js?v=1701102786'></script>
<script src='/training-material/assets/js/bundle.03aefefa.js?v=1701105684'></script>

</body>
</html>
63 changes: 49 additions & 14 deletions all-faq.html
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9 changes: 5 additions & 4 deletions api/configuration.json
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"resources": [
"assets/js/theme.js"
],
"timestamp": 1701102786,
"timestamp": 1701105684,
"hash": "f1f2de89",
"path": "/assets/js/bundle.f1f2de89.js"
},
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"assets/js/[email protected]",
"assets/js/main.js"
],
"timestamp": 1701102786,
"timestamp": 1701105684,
"hash": "03aefefa",
"path": "/assets/js/bundle.03aefefa.js"
}
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"cofest": "fas fa-users",
"comment": "far fa-comment-dots",
"congratulations": "far fa-thumbs-up",
"copy": "far fa-copy",
"curriculum": "fas fa-graduation-cap",
"details": "fas fa-info-circle",
"docker_image": "fab fa-docker",
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"serving": false,
"boxify": {
},
"git_revision": "98e1a6aedea81f92ce802571fef5d1f900f68f46",
"git_revision_short": "98e1a6a",
"git_revision": "def5a1967ee4b3dfe2d49aa3c15eef271d572f3b",
"git_revision_short": "def5a19",
"gtn_fork": "galaxyproject",
"git_tags": [
"2019-02-07",
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11 changes: 0 additions & 11 deletions api/ga4gh/trs/v2/tools/assembly-vgp_workflow_training/versions/main_workflow.json
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7 changes: 0 additions & 7 deletions ...trs/v2/tools/assembly-vgp_workflow_training/versions/main_workflow/GALAXY/descriptor.json
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14 changes: 14 additions & 0 deletions api/gtn.bib
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Expand Up @@ -1862,6 +1862,20 @@ @article{Lariviere2022
journal = {Galaxy Training Network},
month_numeric = {3}
}
@article{Guan2020-st,
title = {Identifying and removing haplotypic duplication in primary genome assemblies},
author = {Guan, Dengfeng and McCarthy, Shane A and Wood, Jonathan and Howe, Kerstin and Wang, Yadong and Durbin, Richard},
abstract = {MOTIVATION: Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors. RESULTS: Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines. AVAILABILITY AND IMPLEMENTATION: The source code is written in C and is available at https://github.com/dfguan/purge_dups. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
doi = {10.1093/bioinformatics/btaa025},
journal = {Bioinformatics},
volume = {36},
number = {9},
pages = {2896–2898},
month = may,
year = {2020},
language = {en},
month_numeric = {5}
}
@book{Fisher2015,
author = {},
title = {Taking off the training wheels: the properties of a dynamic vegetation model without climate envelopes, CLM4.5(ED)},
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2 changes: 1 addition & 1 deletion api/psl.json
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