Added Ng entry

naobservatory · May 1, 2024 · 6672da9 · 6672da9
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diff --git a/data/2024-05-01_ng/adapters.fasta b/data/2024-05-01_ng/adapters.fasta
@@ -0,0 +1,41 @@
+>0
+GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>1
+TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>2
+unspecified
+>3
+heifigepsna
+>4
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>5
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>6
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+>7
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>8
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC
+T
+>9
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>10
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC
+>11
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>12
+GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>13
+CAAGCAGAAGACGGCATACGAGAT
+>14
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>15
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>16
+CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>17
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>18
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>19
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
diff --git a/data/2024-05-01_ng/hv_clade_counts.tsv.gz b/data/2024-05-01_ng/hv_clade_counts.tsv.gz
diff --git a/data/2024-05-01_ng/hv_hits_blast_paired.tsv.gz b/data/2024-05-01_ng/hv_hits_blast_paired.tsv.gz
diff --git a/data/2024-05-01_ng/hv_hits_putative_filtered.tsv.gz b/data/2024-05-01_ng/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-05-01_ng/kraken_reports.tsv.gz b/data/2024-05-01_ng/kraken_reports.tsv.gz
diff --git a/data/2024-05-01_ng/qc_adapter_stats.tsv.gz b/data/2024-05-01_ng/qc_adapter_stats.tsv.gz
diff --git a/data/2024-05-01_ng/qc_basic_stats.tsv.gz b/data/2024-05-01_ng/qc_basic_stats.tsv.gz
diff --git a/data/2024-05-01_ng/qc_quality_base_stats.tsv.gz b/data/2024-05-01_ng/qc_quality_base_stats.tsv.gz
diff --git a/data/2024-05-01_ng/qc_quality_sequence_stats.tsv.gz b/data/2024-05-01_ng/qc_quality_sequence_stats.tsv.gz
diff --git a/data/2024-05-01_ng/sample-metadata.csv b/data/2024-05-01_ng/sample-metadata.csv
@@ -0,0 +1,37 @@
+library,sample,sample_type,date,bioproject,dataset
+SRR6837549,SRR6837549,Effluent from Secondary Settling Tank (SST),2016-10,PRJNA438174,Ng 2019
+SRR6837550,SRR6837550,Effluent from Membrane Biorector (MBR),2016-10,PRJNA438174,Ng 2019
+SRR6837551,SRR6837551,Effluent from Primary Settling Tank (PST),2016-10,PRJNA438174,Ng 2019
+SRR6837552,SRR6837552,Influent,2016-10,PRJNA438174,Ng 2019
+SRR6837553,SRR6837553,Effluent from Primary Settling Tank (PST),2016-11,PRJNA438174,Ng 2019
+SRR6837554,SRR6837554,Influent,2016-11,PRJNA438174,Ng 2019
+SRR6837555,SRR6837555,Sludge (SLUDGE),2016-10,PRJNA438174,Ng 2019
+SRR6837556,SRR6837556,Effluent from Wet Well (WW),2016-10,PRJNA438174,Ng 2019
+SRR6837557,SRR6837557,Effluent from Secondary Settling Tank (SST),2016-11,PRJNA438174,Ng 2019
+SRR6837558,SRR6837558,Effluent from Membrane Biorector (MBR),2016-11,PRJNA438174,Ng 2019
+SRR6837559,SRR6837559,Influent,2017-05,PRJNA438174,Ng 2019
+SRR6837560,SRR6837560,Effluent from Primary Settling Tank (PST),2017-05,PRJNA438174,Ng 2019
+SRR6837561,SRR6837561,Effluent from Membrane Biorector (MBR),2017-05,PRJNA438174,Ng 2019
+SRR6837562,SRR6837562,Effluent from Secondary Settling Tank (SST),2017-05,PRJNA438174,Ng 2019
+SRR6837563,SRR6837563,Effluent from Membrane Biorector (MBR),2017-03,PRJNA438174,Ng 2019
+SRR6837564,SRR6837564,Effluent from Secondary Settling Tank (SST),2017-03,PRJNA438174,Ng 2019
+SRR6837565,SRR6837565,Effluent from Wet Well (WW),2017-03,PRJNA438174,Ng 2019
+SRR6837566,SRR6837566,Sludge (SLUDGE),2017-03,PRJNA438174,Ng 2019
+SRR6837567,SRR6837567,Effluent from Membrane Biorector (MBR),2017-08,PRJNA438174,Ng 2019
+SRR6837568,SRR6837568,Effluent from Wet Well (WW),2017-05,PRJNA438174,Ng 2019
+SRR6837569,SRR6837569,Sludge (SLUDGE),2017-05,PRJNA438174,Ng 2019
+SRR6837570,SRR6837570,Effluent from Secondary Settling Tank (SST),2017-08,PRJNA438174,Ng 2019
+SRR6837571,SRR6837571,Sludge (SLUDGE),2016-11,PRJNA438174,Ng 2019
+SRR6837572,SRR6837572,Effluent from Wet Well (WW),2016-11,PRJNA438174,Ng 2019
+SRR6837573,SRR6837573,Effluent from Primary Settling Tank (PST),2017-01,PRJNA438174,Ng 2019
+SRR6837574,SRR6837574,Influent,2017-01,PRJNA438174,Ng 2019
+SRR6837575,SRR6837575,Effluent from Secondary Settling Tank (SST),2017-01,PRJNA438174,Ng 2019
+SRR6837576,SRR6837576,Effluent from Membrane Biorector (MBR),2017-01,PRJNA438174,Ng 2019
+SRR6837577,SRR6837577,Sludge (SLUDGE),2017-01,PRJNA438174,Ng 2019
+SRR6837578,SRR6837578,Effluent from Wet Well (WW),2017-01,PRJNA438174,Ng 2019
+SRR6837579,SRR6837579,Effluent from Primary Settling Tank (PST),2017-03,PRJNA438174,Ng 2019
+SRR6837580,SRR6837580,Influent,2017-03,PRJNA438174,Ng 2019
+SRR6837581,SRR6837581,Effluent from Primary Settling Tank (PST),2017-08,PRJNA438174,Ng 2019
+SRR6837582,SRR6837582,Influent,2017-08,PRJNA438174,Ng 2019
+SRR6837583,SRR6837583,Sludge (SLUDGE),2017-08,PRJNA438174,Ng 2019
+SRR6837584,SRR6837584,Effluent from Wet Well (WW),2017-08,PRJNA438174,Ng 2019
diff --git a/data/2024-05-01_ng/taxid-names.tsv.gz b/data/2024-05-01_ng/taxid-names.tsv.gz
@@ -0,0 +1 @@
+../2024-04-01_spurbeck/taxid-names.tsv.gz
diff --git a/data/2024-05-01_ng/taxonomic_composition.tsv.gz b/data/2024-05-01_ng/taxonomic_composition.tsv.gz
diff --git a/data/2024-05-01_ng/viral-taxids.tsv.gz b/data/2024-05-01_ng/viral-taxids.tsv.gz
@@ -0,0 +1 @@
+../2024-03-19_brumfield/viral-taxids.tsv.gz
diff --git a/docs/img/2024-05-01_ng-schematic.png b/docs/img/2024-05-01_ng-schematic.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/listings.json b/docs/listings.json
@@ -2,6 +2,7 @@
   {
     "listing": "/index.html",
     "items": [
+      "/notebooks/2024-05-01_ng.html",
       "/notebooks/2024-05-01_bengtsson-palme.html",
       "/notebooks/2024-04-30_brinch.html",
       "/notebooks/2024-04-19_leung.html",

diff --git a/docs/notebooks/2024-05-01_bengtsson-palme.html b/docs/notebooks/2024-05-01_bengtsson-palme.html
@@ -6,7 +6,7 @@
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 <meta name="author" content="Will Bradshaw">
 <meta name="dcterms.date" content="2024-05-01">
-<title>Will’s Public NAO Notebook - Workflow analysis of Bengtsson-Palme et al.&nbsp;(2021)</title>
+<title>Will’s Public NAO Notebook - Workflow analysis of Bengtsson-Palme et al.&nbsp;(2016)</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -145,7 +145,7 @@
       </div> <!-- /container-fluid -->
     </nav></header><!-- content --><header id="title-block-header" class="quarto-title-block default page-columns page-full"><div class="quarto-title-banner page-columns page-full">
     <div class="quarto-title column-body">
-      <div class="quarto-title-block"><div><h1 class="title">Workflow analysis of Bengtsson-Palme et al.&nbsp;(2021)</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>
+      <div class="quarto-title-block"><div><h1 class="title">Workflow analysis of Bengtsson-Palme et al.&nbsp;(2016)</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 grab samples from Sweden.</p>
                       </div>
   </div>
@@ -275,7 +275,7 @@
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 <div class="sourceCode" id="cb51" data-shortcodes="false"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb51-1"><a href="#cb51-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
-<span id="cb51-2"><a href="#cb51-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Workflow analysis of Bengtsson-Palme et al. (2021)"</span></span>
+<span id="cb51-2"><a href="#cb51-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Workflow analysis of Bengtsson-Palme et al. (2016)"</span></span>
 <span id="cb51-3"><a href="#cb51-3" aria-hidden="true" tabindex="-1"></a><span class="an">subtitle:</span><span class="co"> "Wastewater grab samples from Sweden."</span></span>
 <span id="cb51-4"><a href="#cb51-4" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> "Will Bradshaw"</span></span>
 <span id="cb51-5"><a href="#cb51-5" aria-hidden="true" tabindex="-1"></a><span class="an">date:</span><span class="co"> 2024-05-01</span></span>
@@ -2279,7 +2279,7 @@
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diff --git a/docs/notebooks/2024-05-01_bengtsson-palme_files/figure-html/plot-basic-stats-1.png b/docs/notebooks/2024-05-01_bengtsson-palme_files/figure-html/plot-basic-stats-1.png