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hexylena committed Jul 10, 2023
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12 changes: 6 additions & 6 deletions 404.html
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<script type="text/javascript">
Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@5dc0431525782783a521c975716b93c27022522d",
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sampleRate: 0.1,
tracesSampleRate: 0.1,
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<link rel="manifest" href="/training-material/manifest.json">
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</head>
<body data-spy="scroll" data-target="#toc">
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<header>
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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>
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Revision <a href="https://github.com/galaxyproject/training-material/commit/5dc0431525782783a521c975716b93c27022522d">5dc0431</a>, built with Jekyll (4.3.2 | production)
Revision <a href="https://github.com/galaxyproject/training-material/commit/5df6976efa1daea8d272f72a2e2f00265343347e">5df6976</a>, built with Jekyll (4.3.2 | production)
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12 changes: 6 additions & 6 deletions accessibility.html
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<script type="text/javascript">
Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@5dc0431525782783a521c975716b93c27022522d",
release: "galaxy-training-network@5df6976efa1daea8d272f72a2e2f00265343347e",
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>
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<link rel="stylesheet" href="/training-material/assets/css/main.css?v=3">
<link rel="manifest" href="/training-material/manifest.json">
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</head>
<body data-spy="scroll" data-target="#toc">
<script src='/training-material/assets/js/bundle.theme.js?v=1688947810'></script>
<script src='/training-material/assets/js/bundle.theme.js?v=1688990776'></script>
<header>
<nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
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Expand Down Expand Up @@ -283,7 +283,7 @@ <h3 id="additional-features">Additional Features</h3>
The GTN infrastructure is licensed under <a rel="license" href="https://github.com/galaxyproject/training-material/blob/main/LICENSE.md">MIT</a>
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<p>
Revision <a href="https://github.com/galaxyproject/training-material/commit/5dc0431525782783a521c975716b93c27022522d">5dc0431</a>, built with Jekyll (4.3.2 | production)
Revision <a href="https://github.com/galaxyproject/training-material/commit/5df6976efa1daea8d272f72a2e2f00265343347e">5df6976</a>, built with Jekyll (4.3.2 | production)
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</footer>


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21 changes: 14 additions & 7 deletions all-faq.html
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<script type="text/javascript">
Sentry.init({
dsn: "https://[email protected]/10",
release: "galaxy-training-network@5dc0431525782783a521c975716b93c27022522d",
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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>
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<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">
<script src='/training-material/assets/js/bundle.theme.js?v=1688947810'></script>
<script src='/training-material/assets/js/bundle.theme.js?v=1688990776'></script>
<header>
<nav class="navbar navbar-expand-md navbar-dark" aria-label="Site Navigation">
<div class="container">
Expand Down Expand Up @@ -1921,6 +1921,13 @@ <h4 class="faq-area"> Kraken2 and the k-mer approach for taxonomy classification



<h4 class="faq-area"> Quality Scores <a href="/training-material/topics/sequence-analysis/faqs/quality_score.html"><i class="fas fa-external-link-alt"></i></a> </h4>

<!--SNIPPET--><blockquote class="details"> <div class="box-title details-title" id="details-quality-scores"><button class="gtn-boxify-button details" type="button" aria-controls="details-quality-scores" aria-expanded="true"><i class="fas fa-info-circle" aria-hidden="true"></i> Details: Quality Scores<span class="fold-unfold fa fa-minus-square"></span></button></div> <p>But what does this quality score mean?</p> <p>The quality score for each sequence is a string of characters, one for each base of the nucleotide sequence, used to characterize the probability of misidentification of each base. The score is encoded using the ASCII character table (with <a href="https://en.wikipedia.org/wiki/FASTQ_format#Encoding">some historical differences</a>):</p> <p>To save space, the sequencer records an <a href="http://drive5.com/usearch/manual/quality_score.html">ASCII character</a> to represent scores 0-42. For example 10 corresponds to “+” and 40 corresponds to “I”. FastQC knows how to translate this. This is often called “Phred” scoring.</p> <p><img src="/training-material/topics/sequence-analysis/faqs/images/fastq-quality-encoding.png" alt="Encoding of the quality score with ASCII characters for different Phred encoding. The ascii code sequence is shown at the top with symbols for 33 to 64, upper case letters, more symbols, and then lowercase letters. Sanger maps from 33 to 73 while solexa is shifted, starting at 59 and going to 104. Illumina 1.3 starts at 54 and goes to 104, Illumina 1.5 is shifted three scores to the right but still ends at 104. Illumina 1.8+ goes back to the Sanger except one single score wider. Illumina" /></p> <p>So there is an ASCII character associated with each nucleotide, representing its <a href="https://en.wikipedia.org/wiki/Phred_quality_score">Phred quality score</a>, the probability of an incorrect base call:</p> <table> <thead> <tr> <th>Phred Quality Score</th> <th>Probability of incorrect base call</th> <th>Base call accuracy</th> </tr> </thead> <tbody> <tr> <td>10</td> <td>1 in 10</td> <td>90%</td> </tr> <tr> <td>20</td> <td>1 in 100</td> <td>99%</td> </tr> <tr> <td>30</td> <td>1 in 1000</td> <td>99.9%</td> </tr> <tr> <td>40</td> <td>1 in 10,000</td> <td>99.99%</td> </tr> <tr> <td>50</td> <td>1 in 100,000</td> <td>99.999%</td> </tr> <tr> <td>60</td> <td>1 in 1,000,000</td> <td>99.9999%</td> </tr> </tbody> </table> <p>What does 0-42 represent? These numbers, when plugged into a formula, tell us the probability of an error for that base. This is the formula, where Q is our quality score (0-42) and P is the probability of an error:</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Q = -10 log10(P)<br></code></pre></div></div> <p>Using this formula, we can calculate that a quality score of 40 means only 0.00010 probability of an error!</p> </blockquote> <!--END_SNIPPET-->




<h4 class="faq-area"> What is Taxonomy? <a href="/training-material/topics/metagenomics/faqs/taxon.html"><i class="fas fa-external-link-alt"></i></a> </h4>

<!--SNIPPET--><blockquote class="details"> <div class="box-title details-title" id="details-what-is-taxonomy"><button class="gtn-boxify-button details" type="button" aria-controls="details-what-is-taxonomy" aria-expanded="true"><i class="fas fa-info-circle" aria-hidden="true"></i> Details: What is Taxonomy?<span class="fold-unfold fa fa-minus-square"></span></button></div> <p>Taxonomy is the method used to naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics such as morphological characteristics, phylogenetic characteristics, DNA data, etc. It is founded on the concept that the similarities descend from a common evolutionary ancestor.</p> <p>Defined groups of organisms are known as <strong>taxa</strong>. Taxa are given a taxonomic rank and are aggregated into super groups of higher rank to create a taxonomic hierarchy. The taxonomic hierarchy includes eight levels: <strong>Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species.</strong></p> <p><img src="/training-material/topics/metagenomics/faqs/images/taxonomy.png" alt="Example of taxonomy. It starts, top to bottom, with Kingdom &quot;Animalia&quot;, Phylum &quot;Chordata&quot;, Class &quot;Mammalia&quot;, and Order &quot;Carnivora&quot;. Then it splits in 3. On the left, Family &quot;Felidae&quot;, with 2 genus &quot;Felis&quot; and &quot;Panthera&quot; and below 3 species &quot;F. catus&quot; and &quot;F. pardalis&quot; below &quot;Felis&quot;, &quot;P. pardus&quot; below &quot;Panthera&quot;. In the middle, Family &quot;Canidae&quot;, genus &quot;Canis&quot; and 2 species &quot;C. familiaris&quot; and &quot;C. lupus&quot;. On the right, Family &quot;Ursidae&quot;, Genus &quot;Ursus&quot; and 2 species &quot;U. arctos&quot; and &quot;U. horribilus&quot;. Below each species is a illustration of the species" /></p> <p>The classification system begins with <strong>3 domains</strong> that encompass all living and extinct forms of life</p> <ul> <li>The <strong>Bacteria</strong> and <strong>Archae</strong> are mostly microscopic, but quite widespread.</li> <li>Domain <strong>Eukarya</strong> contains more complex organisms</li> </ul> <p>When new species are found, they are assigned into taxa in the taxonomic hierarchy. For example for the cat:</p> <table> <thead> <tr> <th>Level</th> <th>Classification</th> </tr> </thead> <tbody> <tr> <td>Domain</td> <td>Eukaryota</td> </tr> <tr> <td>Kingdom</td> <td>Animalia</td> </tr> <tr> <td>Phylum</td> <td>Chordata</td> </tr> <tr> <td>Class</td> <td>Mammalia</td> </tr> <tr> <td>Order</td> <td>Carnivora</td> </tr> <tr> <td>Family</td> <td>Felidae</td> </tr> <tr> <td>Genus</td> <td><em>Felis</em></td> </tr> <tr> <td>Species</td> <td><em>F. catus</em></td> </tr> </tbody> </table> <p>From this classification, one can generate a tree of life, also known as a phylogenetic tree. It is a rooted tree that describes the relationship of all life on earth. At the root sits the “last universal common ancestor” and the three main branches (in taxonomy also called domains) are bacteria, archaea and eukaryotes. Most important for this is the idea that all life on earth is derived from a common ancestor and therefore when comparing two species, you will -sooner or later- find a common ancestor for all of them.</p> <p>Let’s explore taxonomy in the Tree of Life, using <a href="https://lifemap.univ-lyon1.fr/">Lifemap</a></p> <iframe id="Lifemap" src="https://lifemap.univ-lyon1.fr/explore.html" frameborder="0" width="100%" height="600px"></iframe> </blockquote> <!--END_SNIPPET-->
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<h4 class="faq-area"> GTN Stats <a href="/training-material/faqs/gtn/gtn_stats.html"><i class="fas fa-external-link-alt"></i></a> </h4>

<!--SNIPPET--> <!-- tutorial stats --> <div class="row" style="color: var(--text-color-boxtitle)"> <div class="col-md-4"> <div class="gtn-card color-agenda"> <div class="card-title">37</div> <div class="card-text">Topics</div> </div> </div> <div class="col-md-4"> <div class="gtn-card color-tip"> <div class="card-title">358</div> <div class="card-text">Tutorials</div> </div> </div> <div class="col-md-4"> <div class="gtn-card color-details"> <div class="card-title">390</div> <div class="card-text"><abbr title="Frequently Asked Questions">FAQs</abbr></div> </div> </div> <div class="col-md-6"> <div class="gtn-card color-comment"> <div class="card-title">310</div> <div class="card-text">Contributors</div> </div> </div> <div class="col-md-6"> <div class="gtn-card color-handson"> <div class="card-title">8.0</div> <div class="card-text">Years</div> </div> </div> </div> <!--END_SNIPPET-->
<!--SNIPPET--> <!-- tutorial stats --> <div class="row" style="color: var(--text-color-boxtitle)"> <div class="col-md-4"> <div class="gtn-card color-agenda"> <div class="card-title">37</div> <div class="card-text">Topics</div> </div> </div> <div class="col-md-4"> <div class="gtn-card color-tip"> <div class="card-title">359</div> <div class="card-text">Tutorials</div> </div> </div> <div class="col-md-4"> <div class="gtn-card color-details"> <div class="card-title">391</div> <div class="card-text"><abbr title="Frequently Asked Questions">FAQs</abbr></div> </div> </div> <div class="col-md-6"> <div class="gtn-card color-comment"> <div class="card-title">320</div> <div class="card-text">Contributors</div> </div> </div> <div class="col-md-6"> <div class="gtn-card color-handson"> <div class="card-title">8.0</div> <div class="card-text">Years</div> </div> </div> </div> <!--END_SNIPPET-->



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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/5dc0431525782783a521c975716b93c27022522d">5dc0431</a>, built with Jekyll (4.3.2 | production)
Revision <a href="https://github.com/galaxyproject/training-material/commit/5df6976efa1daea8d272f72a2e2f00265343347e">5df6976</a>, built with Jekyll (4.3.2 | production)
</p>
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8 changes: 4 additions & 4 deletions api/configuration.json
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"resources": [
"assets/js/theme.js"
],
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"timestamp": 1688990776
},
"main": {
"preload": true,
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"assets/js/list.min.js",
"assets/js/main.js"
],
"timestamp": 1688947810
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},
"figurify": {
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"boxify": {
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"git_revision": "5dc0431525782783a521c975716b93c27022522d",
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"git_revision": "5df6976efa1daea8d272f72a2e2f00265343347e",
"git_revision_short": "5df6976",
"gtn_fork": "galaxyproject",
"git_tags": [
"2019-02-07",
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