Fixed error in Munk entry

docs/index.html

@@ -165,18 +165,18 @@
 
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-<a href="./notebooks/2024-05-07_munk.html" class="no-external">Workflow analysis of Maritz et al.&nbsp;(2019)</a>
+<a href="./notebooks/2024-05-07_munk.html" class="no-external">Workflow analysis of Munk et al.&nbsp;(2022)</a>
 </h3>
 <div class="listing-subtitle">
-<a href="./notebooks/2024-05-07_munk.html" class="no-external">Wastewater from NYC.</a>
+<a href="./notebooks/2024-05-07_munk.html" class="no-external">A global wastewater study.</a>
 </div>
 </div>
 <div class="metadata">

docs/notebooks/2024-05-07_munk.html

@@ -6,7 +6,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Will Bradshaw">
 <meta name="dcterms.date" content="2024-05-07">
-<title>Will’s Public NAO Notebook - Workflow analysis of Maritz et al.&nbsp;(2019)</title>
+<title>Will’s Public NAO Notebook - Workflow analysis of Munk et al.&nbsp;(2022)</title>
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@@ -145,8 +145,8 @@
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-      <div class="quarto-title-block"><div><h1 class="title">Workflow analysis of Maritz et al.&nbsp;(2019)</h1><button type="button" class="btn code-tools-button dropdown-toggle" id="quarto-code-tools-menu" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi"></i> Code</button><ul class="dropdown-menu dropdown-menu-end" aria-labelelledby="quarto-code-tools-menu"><li><a id="quarto-show-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Show All Code</a></li><li><a id="quarto-hide-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Hide All Code</a></li><li><hr class="dropdown-divider"></li><li><a id="quarto-view-source" class="dropdown-item" href="javascript:void(0)" role="button">View Source</a></li></ul></div></div>
-            <p class="subtitle lead">Wastewater from NYC.</p>
+      <div class="quarto-title-block"><div><h1 class="title">Workflow analysis of Munk et al.&nbsp;(2022)</h1><button type="button" class="btn code-tools-button dropdown-toggle" id="quarto-code-tools-menu" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi"></i> Code</button><ul class="dropdown-menu dropdown-menu-end" aria-labelelledby="quarto-code-tools-menu"><li><a id="quarto-show-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Show All Code</a></li><li><a id="quarto-hide-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Hide All Code</a></li><li><hr class="dropdown-divider"></li><li><a id="quarto-view-source" class="dropdown-item" href="javascript:void(0)" role="button">View Source</a></li></ul></div></div>
+            <p class="subtitle lead">A global wastewater study.</p>
                       </div>
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-<span id="cb49-2"><a href="#cb49-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Workflow analysis of Maritz et al. (2019)"</span></span>
-<span id="cb49-3"><a href="#cb49-3" aria-hidden="true" tabindex="-1"></a><span class="an">subtitle:</span><span class="co"> "Wastewater from NYC."</span></span>
+<span id="cb49-2"><a href="#cb49-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Workflow analysis of Munk et al. (2022)"</span></span>
+<span id="cb49-3"><a href="#cb49-3" aria-hidden="true" tabindex="-1"></a><span class="an">subtitle:</span><span class="co"> "A global wastewater study."</span></span>
 <span id="cb49-4"><a href="#cb49-4" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> "Will Bradshaw"</span></span>
 <span id="cb49-5"><a href="#cb49-5" aria-hidden="true" tabindex="-1"></a><span class="an">date:</span><span class="co"> 2024-05-07</span></span>
 <span id="cb49-6"><a href="#cb49-6" aria-hidden="true" tabindex="-1"></a><span class="an">format:</span></span>

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@@ -32,7 +32,7 @@
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     "title": "Will's Public NAO Notebook",
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-    "text": "Workflow analysis of Maritz et al. (2019)\n\n\nWastewater from NYC.\n\n\n\n\n\nMay 7, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Ng et al. (2019)\n\n\nWastewater from Singapore.\n\n\n\n\n\nMay 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Bengtsson-Palme et al. (2016)\n\n\nWastewater grab samples from Sweden.\n\n\n\n\n\nMay 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Maritz et al. (2019)\n\n\nWastewater from NYC.\n\n\n\n\n\nMay 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Brinch et al. (2020)\n\n\nWastewater from Copenhagen.\n\n\n\n\n\nApr 30, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Leung et al. (2021)\n\n\nAir sampling from urban public transit systems.\n\n\n\n\n\nApr 19, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Rosario et al. (2018)\n\n\nAir sampling from a student dorm in Colorado.\n\n\n\n\n\nApr 12, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Prussin et al. (2019)\n\n\nAir filters from a daycare in Virginia.\n\n\n\n\n\nApr 12, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Brumfield et al. (2022)\n\n\nWastewater from a manhole in Maryland.\n\n\n\n\n\nApr 8, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Spurbeck et al. (2023)\n\n\nCave carpa.\n\n\n\n\n\nApr 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nFollowup analysis of Yang et al. (2020)\n\n\nDigging into deduplication.\n\n\n\n\n\nMar 19, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Yang et al. (2020)\n\n\nWastewater from Xinjiang.\n\n\n\n\n\nMar 16, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nImproving read deduplication in the MGS workflow\n\n\nRemoving reverse-complement duplicates of human-viral reads.\n\n\n\n\n\nMar 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Rothman et al. (2021), part 2\n\n\nPanel-enriched samples.\n\n\n\n\n\nFeb 29, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Rothman et al. (2021), part 1\n\n\nUnenriched samples.\n\n\n\n\n\nFeb 27, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Crits-Christoph et al. (2021), part 3\n\n\nFixing the virus pipeline.\n\n\n\n\n\nFeb 15, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Crits-Christoph et al. (2021), part 2\n\n\nAbundance and composition of human-infecting viruses.\n\n\n\n\n\nFeb 8, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Crits-Christoph et al. (2021), part 1\n\n\nPreprocessing and composition.\n\n\n\n\n\nFeb 4, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nAutomating BLAST validation of human viral read assignment\n\n\nExperiments with BLASTN remote mode\n\n\n\n\n\nJan 30, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nProject Runway RNA-seq testing data: removing livestock reads\n\n\n\n\n\n\n\n\nDec 22, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Project Runway RNA-seq testing data\n\n\nApplying a new workflow to some oldish data.\n\n\n\n\n\nDec 19, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nEstimating the effect of read depth on duplication rate for Project Runway DNA data\n\n\nHow deep can we go?\n\n\n\n\n\nNov 8, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing viral read assignments between pipelines on Project Runway data\n\n\n\n\n\n\n\n\nNov 2, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nInitial analysis of Project Runway protocol testing data\n\n\n\n\n\n\n\n\nOct 31, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing options for read deduplication\n\n\nClumpify vs fastp\n\n\n\n\n\nOct 19, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing Ribodetector and bbduk for rRNA detection\n\n\nIn search of quick rRNA filtering.\n\n\n\n\n\nOct 16, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing FASTP and AdapterRemoval for MGS pre-processing\n\n\nTwo tools – how do they perform?\n\n\n\n\n\nOct 12, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nHow does Element AVITI sequencing work?\n\n\nFindings of a shallow investigation\n\n\n\n\n\nOct 11, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nExtraction experiment 2: high-level results & interpretation\n\n\nComparing RNA yields and quality across extraction kits for settled solids\n\n\n\n\n\nSep 21, 2023\n\n\n\n\n\n\nNo matching items"
+    "text": "Workflow analysis of Munk et al. (2022)\n\n\nA global wastewater study.\n\n\n\n\n\nMay 7, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Ng et al. (2019)\n\n\nWastewater from Singapore.\n\n\n\n\n\nMay 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Bengtsson-Palme et al. (2016)\n\n\nWastewater grab samples from Sweden.\n\n\n\n\n\nMay 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Maritz et al. (2019)\n\n\nWastewater from NYC.\n\n\n\n\n\nMay 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Brinch et al. (2020)\n\n\nWastewater from Copenhagen.\n\n\n\n\n\nApr 30, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Leung et al. (2021)\n\n\nAir sampling from urban public transit systems.\n\n\n\n\n\nApr 19, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Rosario et al. (2018)\n\n\nAir sampling from a student dorm in Colorado.\n\n\n\n\n\nApr 12, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Prussin et al. (2019)\n\n\nAir filters from a daycare in Virginia.\n\n\n\n\n\nApr 12, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Brumfield et al. (2022)\n\n\nWastewater from a manhole in Maryland.\n\n\n\n\n\nApr 8, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Spurbeck et al. (2023)\n\n\nCave carpa.\n\n\n\n\n\nApr 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nFollowup analysis of Yang et al. (2020)\n\n\nDigging into deduplication.\n\n\n\n\n\nMar 19, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Yang et al. (2020)\n\n\nWastewater from Xinjiang.\n\n\n\n\n\nMar 16, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nImproving read deduplication in the MGS workflow\n\n\nRemoving reverse-complement duplicates of human-viral reads.\n\n\n\n\n\nMar 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Rothman et al. (2021), part 2\n\n\nPanel-enriched samples.\n\n\n\n\n\nFeb 29, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Rothman et al. (2021), part 1\n\n\nUnenriched samples.\n\n\n\n\n\nFeb 27, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Crits-Christoph et al. (2021), part 3\n\n\nFixing the virus pipeline.\n\n\n\n\n\nFeb 15, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Crits-Christoph et al. (2021), part 2\n\n\nAbundance and composition of human-infecting viruses.\n\n\n\n\n\nFeb 8, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Crits-Christoph et al. (2021), part 1\n\n\nPreprocessing and composition.\n\n\n\n\n\nFeb 4, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nAutomating BLAST validation of human viral read assignment\n\n\nExperiments with BLASTN remote mode\n\n\n\n\n\nJan 30, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nProject Runway RNA-seq testing data: removing livestock reads\n\n\n\n\n\n\n\n\nDec 22, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nWorkflow analysis of Project Runway RNA-seq testing data\n\n\nApplying a new workflow to some oldish data.\n\n\n\n\n\nDec 19, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nEstimating the effect of read depth on duplication rate for Project Runway DNA data\n\n\nHow deep can we go?\n\n\n\n\n\nNov 8, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing viral read assignments between pipelines on Project Runway data\n\n\n\n\n\n\n\n\nNov 2, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nInitial analysis of Project Runway protocol testing data\n\n\n\n\n\n\n\n\nOct 31, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing options for read deduplication\n\n\nClumpify vs fastp\n\n\n\n\n\nOct 19, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing Ribodetector and bbduk for rRNA detection\n\n\nIn search of quick rRNA filtering.\n\n\n\n\n\nOct 16, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nComparing FASTP and AdapterRemoval for MGS pre-processing\n\n\nTwo tools – how do they perform?\n\n\n\n\n\nOct 12, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nHow does Element AVITI sequencing work?\n\n\nFindings of a shallow investigation\n\n\n\n\n\nOct 11, 2023\n\n\n\n\n\n\n\n\n\n\n\n\nExtraction experiment 2: high-level results & interpretation\n\n\nComparing RNA yields and quality across extraction kits for settled solids\n\n\n\n\n\nSep 21, 2023\n\n\n\n\n\n\nNo matching items"
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@@ -338,14 +338,14 @@
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-    "title": "Workflow analysis of Maritz et al. (2019)",
+    "title": "Workflow analysis of Munk et al. (2022)",
     "section": "",
     "text": "The final dataset from the P2RA dataset I want to analyze here is Munk et al. (2022), an enormous dataset of >1,000 raw influent samples from 101 countries collected between 2016 and 2019. As in previous DNA studies like Bengtsson-Palme, samples were centrifuged and only the pellet was retained for sequencing, so we expect viral abundance to be low; nevertheless, this is the largest and most comprehensive DNA wastewater dataset we’ve been able to find to date, so it’s worth having a look at what’s in it. The pellet from each sample was resuspended, was homogenized with bead-beating, underwent DNA extraction and library prep, and was sequenced using Illumina technology; earlier samples were sequenced on an Illumina HiSeq3000, while later samples were sequenced on a NovaSeq6000, both with 2x150bp reads."
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-    "title": "Workflow analysis of Maritz et al. (2019)",
+    "title": "Workflow analysis of Munk et al. (2022)",
     "section": "Footnotes",
     "text": "Footnotes\n\nI wasn’t able to quickly find any HDI datasets other than the most recent one, and it didn’t seem worth doing serious digging for this quick analysis.↩︎"
   }

notebooks/2024-05-07_munk.qmd

@@ -1,6 +1,6 @@
 ---
-title: "Workflow analysis of Maritz et al. (2019)"
-subtitle: "Wastewater from NYC."
+title: "Workflow analysis of Munk et al. (2022)"
+subtitle: "A global wastewater study."
 author: "Will Bradshaw"
 date: 2024-05-07
 format: