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accessing-ancient-metagenomic-data.html

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- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Introduction to <em>de novo</em> Genome Assembly</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title"><em>De novo</em> Genome Assembly</span></span></a>
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acknowledgements.html

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- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Introduction to <em>de novo</em> Genome Assembly</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title"><em>De novo</em> Genome Assembly</span></span></a>
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ancient-metagenomic-pipelines.html

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- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Introduction to <em>de novo</em> Genome Assembly</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title"><em>De novo</em> Genome Assembly</span></span></a>
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@@ -1288,9 +1288,8 @@ <h3 data-number="17.4.3" class="anchored" data-anchor-id="prepare-and-run-ameta"
 <div class="sourceCode" id="cb20"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="ex">conda</span> activate aMeta</span>
 <span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> /<span class="op">&lt;</span>path/<span class="op">&lt;</span>to<span class="op">&gt;</span>/ancient-metagenomic-pipelines/aMeta/</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>Finally, we are ready to run aMeta, where it will automatically pick up our config and samplesheet file we placed in <code>config/</code>!</p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="co">#| eval: false</span></span>
-<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a><span class="co">## change conda-frontend to mamba if we set this up earlier!</span></span>
-<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a><span class="ex">snakemake</span> <span class="at">--snakefile</span> workflow/Snakefile <span class="at">--use-conda</span> <span class="at">-j</span> 10 <span class="at">--conda-frontend</span> conda</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="co">## change conda-frontend to mamba if we set this up earlier!</span></span>
+<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a><span class="ex">snakemake</span> <span class="at">--snakefile</span> workflow/Snakefile <span class="at">--use-conda</span> <span class="at">-j</span> 10 <span class="at">--conda-frontend</span> conda</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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@@ -1454,7 +1453,7 @@ <h2 data-number="17.5" class="anchored" data-anchor-id="what-is-nf-coremag"><spa
 <p>Firstly we need a method of validating that contigs are from an ancient genome (in nf-core/mag, damage patterns are generated by <code>pyDamage</code>).</p>
 <p>Secondly, to correct for falsely included damage bases in contigs in some contexts. As previously stated a previous chapter by Alex Hübner:</p>
 <blockquote class="blockquote">
-<p>In our group we realised that the gene sequences that were annotated on the contigs of MEGAHIT tended to have a higher number of nonsense mutations compared to the known variants of the genes. After manual inspection, we observed that many of these mutations appeared because MEGAHIT chose the damage-derived T allele over the C allele or the damage-derived A allele over a G allele <span class="citation" data-cites="Klapper2023-mv">(see <a href="#ref-Klapper2023-mv" role="doc-biblioref"><strong>Klapper2023-mv?</strong></a>)</span>.</p>
+<p>In our group we realised that the gene sequences that were annotated on the contigs of MEGAHIT tended to have a higher number of nonsense mutations compared to the known variants of the genes. After manual inspection, we observed that many of these mutations appeared because MEGAHIT chose the damage-derived T allele over the C allele or the damage-derived A allele over a G allele <span class="citation" data-cites="Klapper2023-nv">(see <a href="#ref-Klapper2023-nv" role="doc-biblioref">Klapper et al. 2023, fig. S1</a>)</span>.</p>
 </blockquote>
 <blockquote class="blockquote">
 <p>To overcome this issue, my colleagues Maxime Borry, James Fellows Yates and I developed a strategy to replace these damage-derived alleles in the contig sequences. This approach consists of aligning the short-read data against the contigs, performing genotyping along them, and finally replacing all alleles for which we have strong support for an allele that is different from the one selected by MEGAHIT.</p>
@@ -1836,6 +1835,9 @@ <h2 data-number="17.8" class="anchored" data-anchor-id="references"><span class=
 <div id="ref-Kim2016-qc" class="csl-entry" role="listitem">
 Kim, Daehwan, Li Song, Florian P Breitwieser, and Steven L Salzberg. 2016. <span>“Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.”</span> <em>Genome Research</em> 26 (12): 1721–29. <a href="https://doi.org/10.1101/gr.210641.116">https://doi.org/10.1101/gr.210641.116</a>.
 </div>
+<div id="ref-Klapper2023-nv" class="csl-entry" role="listitem">
+Klapper, Martin, Alexander Hübner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G Haensch, Shuaibing Zhang, et al. 2023. <span>“Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic.”</span> <em>Science (New York, N.Y.)</em>, May, eadf5300. <a href="https://doi.org/10.1126/science.adf5300">https://doi.org/10.1126/science.adf5300</a>.
+</div>
 <div id="ref-Krakau2022-we" class="csl-entry" role="listitem">
 Krakau, Sabrina, Daniel Straub, Hadrien Gourlé, Gisela Gabernet, and Sven Nahnsen. 2022. <span>“Nf-Core/Mag: A Best-Practice Pipeline for Metagenome Hybrid Assembly and Binning.”</span> <em>NAR Genomics and Bioinformatics</em> 4 (1). <a href="https://doi.org/10.1093/nargab/lqac007">https://doi.org/10.1093/nargab/lqac007</a>.
 </div>

appendices.html

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- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Introduction to <em>de novo</em> Genome Assembly</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title"><em>De novo</em> Genome Assembly</span></span></a>
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