Added Maritz entry

naobservatory · May 1, 2024 · 3ed841a · 3ed841a
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diff --git a/data/2024-05-01_maritz/adapters.fasta b/data/2024-05-01_maritz/adapters.fasta
@@ -0,0 +1,41 @@
+>0
+heifigepsna
+>1
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>2
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>3
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>4
+CAAGCAGAAGACGGCATACGAGAT
+>5
+GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>6
+GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>7
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>8
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>9
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC
+>10
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>11
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>12
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC
+T
+>13
+TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>14
+unspecified
+>15
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>16
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>17
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>18
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+>19
+CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
diff --git a/data/2024-05-01_maritz/hv_clade_counts.tsv.gz b/data/2024-05-01_maritz/hv_clade_counts.tsv.gz
diff --git a/data/2024-05-01_maritz/hv_hits_blast_paired.tsv.gz b/data/2024-05-01_maritz/hv_hits_blast_paired.tsv.gz
diff --git a/data/2024-05-01_maritz/hv_hits_putative_filtered.tsv.gz b/data/2024-05-01_maritz/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-05-01_maritz/kraken_reports.tsv.gz b/data/2024-05-01_maritz/kraken_reports.tsv.gz
diff --git a/data/2024-05-01_maritz/qc_adapter_stats.tsv.gz b/data/2024-05-01_maritz/qc_adapter_stats.tsv.gz
diff --git a/data/2024-05-01_maritz/qc_basic_stats.tsv.gz b/data/2024-05-01_maritz/qc_basic_stats.tsv.gz
diff --git a/data/2024-05-01_maritz/qc_quality_base_stats.tsv.gz b/data/2024-05-01_maritz/qc_quality_base_stats.tsv.gz
diff --git a/data/2024-05-01_maritz/qc_quality_sequence_stats.tsv.gz b/data/2024-05-01_maritz/qc_quality_sequence_stats.tsv.gz
diff --git a/data/2024-05-01_maritz/sample-metadata.csv b/data/2024-05-01_maritz/sample-metadata.csv
@@ -0,0 +1,17 @@
+library,sample,dataset,bioproject
+ERR2729796,NYC-01,Maritz 2019,PRJEB28033
+ERR2729797,NYC-02,Maritz 2019,PRJEB28033
+ERR2729798,NYC-03,Maritz 2019,PRJEB28033
+ERR2729799,NYC-04,Maritz 2019,PRJEB28033
+ERR2729800,NYC-05,Maritz 2019,PRJEB28033
+ERR2729801,NYC-06,Maritz 2019,PRJEB28033
+ERR2729802,NYC-07,Maritz 2019,PRJEB28033
+ERR2729803,NYC-08,Maritz 2019,PRJEB28033
+ERR2729804,NYC-09,Maritz 2019,PRJEB28033
+ERR2729805,NYC-10,Maritz 2019,PRJEB28033
+ERR2729806,NYC-11,Maritz 2019,PRJEB28033
+ERR2729807,NYC-12,Maritz 2019,PRJEB28033
+ERR2729808,NYC-13,Maritz 2019,PRJEB28033
+ERR2729809,NYC-14,Maritz 2019,PRJEB28033
+ERR2729810,NYC-15,Maritz 2019,PRJEB28033
+ERR2729811,NYC-16,Maritz 2019,PRJEB28033
diff --git a/data/2024-05-01_maritz/taxid-names.tsv.gz b/data/2024-05-01_maritz/taxid-names.tsv.gz
@@ -0,0 +1 @@
+../2024-04-01_spurbeck/taxid-names.tsv.gz
diff --git a/data/2024-05-01_maritz/taxonomic_composition.tsv.gz b/data/2024-05-01_maritz/taxonomic_composition.tsv.gz
diff --git a/data/2024-05-01_maritz/viral-taxids.tsv.gz b/data/2024-05-01_maritz/viral-taxids.tsv.gz
@@ -0,0 +1 @@
+../2024-03-19_brumfield/viral-taxids.tsv.gz
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/listings.json b/docs/listings.json
@@ -4,6 +4,7 @@
     "items": [
       "/notebooks/2024-05-01_ng.html",
       "/notebooks/2024-05-01_bengtsson-palme.html",
+      "/notebooks/2024-05-01_maritz.html",
       "/notebooks/2024-04-30_brinch.html",
       "/notebooks/2024-04-19_leung.html",
       "/notebooks/2024-04-12_rosario.html",

diff --git a/docs/notebooks/2024-05-01_maritz.html b/docs/notebooks/2024-05-01_maritz.html
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-blast-hits-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-blast-hits-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-family-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-family-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-adeno-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-adeno-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-herpes-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-herpes-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-papilloma-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-papilloma-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-polyoma-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/hv-species-polyoma-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-basic-stats-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-basic-stats-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-blast-results-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-blast-results-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-composition-all-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-composition-all-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-composition-all-2.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-composition-all-2.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-f1-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-f1-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-hv-ra-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-hv-ra-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-hv-scores-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-hv-scores-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-quality-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-quality-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-quality-2.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-quality-2.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-quality-3.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-quality-3.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-raw-quality-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-raw-quality-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-raw-quality-2.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-raw-quality-2.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-raw-quality-3.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/plot-raw-quality-3.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-dedup-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-dedup-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-dedup-2.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-dedup-2.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-figures-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-figures-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-figures-2.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/preproc-figures-2.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/ra-genera-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/ra-genera-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/ra-hv-past-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/ra-hv-past-1.png
diff --git a/docs/notebooks/2024-05-01_maritz_files/figure-html/viral-class-composition-1.png b/docs/notebooks/2024-05-01_maritz_files/figure-html/viral-class-composition-1.png
diff --git a/docs/notebooks/2024-05-01_ng.html b/docs/notebooks/2024-05-01_ng.html
@@ -574,7 +574,7 @@
 </div>
 </div>
 </div>
-<p>As in previous DNA datasets, the vast majority of classified reads were bacterial in origin. The fraction of virus reads varied substantially between sample types, averaging &lt;0.01% in influent and final effluent but closer to 0.05% in other sample types. Interestingly (though not particularly relevantly for this analysis), the fraction of archaeal reads was much higher in influent than other sample types, in contrast to <a href="https://data.securebio.org/wills-public-notebook/notebooks/2024-05-01_bengtsson-palme.html">Bengtsson-Palme</a> where it was highest in slidge.</p>
+<p>As in previous DNA datasets, the vast majority of classified reads were bacterial in origin. The fraction of virus reads varied substantially between sample types, averaging &lt;0.01% in influent and final effluent but closer to 0.05% in other sample types. Interestingly (though not particularly relevantly for this analysis), the fraction of archaeal reads was much higher in influent than other sample types, in contrast to <a href="https://data.securebio.org/wills-public-notebook/notebooks/2024-05-01_bengtsson-palme.html">Bengtsson-Palme</a> where it was highest in sludge.</p>
 <p>As is common for DNA data, viral reads were overwhelmingly dominated by <em>Caudoviricetes</em> phages, though one wet-well sample contained a substantial fraction of <em>Alsuviricetes</em> (a class of mainly plant pathogens that includes <em>Virgaviridae</em>):</p>
 <div class="cell">
 <details class="code-fold"><summary>Code</summary><div class="sourceCode" id="cb19"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="co"># Get Kraken reports</span></span>
@@ -2151,7 +2151,7 @@
 <span id="cb40-427"><a href="#cb40-427" aria-hidden="true" tabindex="-1"></a>p_reads_summ</span>
 <span id="cb40-428"><a href="#cb40-428" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
 <span id="cb40-429"><a href="#cb40-429" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb40-430"><a href="#cb40-430" aria-hidden="true" tabindex="-1"></a>As in previous DNA datasets, the vast majority of classified reads were bacterial in origin. The fraction of virus reads varied substantially between sample types, averaging <span class="sc">\&lt;</span>0.01% in influent and final effluent but closer to 0.05% in other sample types. Interestingly (though not particularly relevantly for this analysis), the fraction of archaeal reads was much higher in influent than other sample types, in contrast to <span class="co">[</span><span class="ot">Bengtsson-Palme</span><span class="co">](https://data.securebio.org/wills-public-notebook/notebooks/2024-05-01_bengtsson-palme.html)</span> where it was highest in slidge.</span>
+<span id="cb40-430"><a href="#cb40-430" aria-hidden="true" tabindex="-1"></a>As in previous DNA datasets, the vast majority of classified reads were bacterial in origin. The fraction of virus reads varied substantially between sample types, averaging <span class="sc">\&lt;</span>0.01% in influent and final effluent but closer to 0.05% in other sample types. Interestingly (though not particularly relevantly for this analysis), the fraction of archaeal reads was much higher in influent than other sample types, in contrast to <span class="co">[</span><span class="ot">Bengtsson-Palme</span><span class="co">](https://data.securebio.org/wills-public-notebook/notebooks/2024-05-01_bengtsson-palme.html)</span> where it was highest in sludge.</span>
 <span id="cb40-431"><a href="#cb40-431" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb40-432"><a href="#cb40-432" aria-hidden="true" tabindex="-1"></a>As is common for DNA data, viral reads were overwhelmingly dominated by *Caudoviricetes* phages, though one wet-well sample contained a substantial fraction of *Alsuviricetes* (a class of mainly plant pathogens that includes *Virgaviridae*):</span>
 <span id="cb40-433"><a href="#cb40-433" aria-hidden="true" tabindex="-1"></a></span>

diff --git a/docs/search.json b/docs/search.json