Added Bengtsson-Palme entry

naobservatory · May 1, 2024 · 575300a · 575300a
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diff --git a/data/2024-04-30_bengtsson-palme/adapters.fasta b/data/2024-04-30_bengtsson-palme/adapters.fasta
@@ -0,0 +1,65 @@
+>0
+CCTCAAAGTGGTATCCAACCGTTAACTACAAATTAGAAACGTATACGGATCCCCCGGGCC
+>1
+ATCCCCCTCTGAAGACGCGGCCGCGATATCCTGCAGATGCATCCAGTACTAGTATGGCCC
+>2
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>3
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC
+>4
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>5
+GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>6
+unspecified
+>7
+TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
+>8
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>9
+heifigepsna
+>10
+CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACA
+>11
+GGCCCGGGGGATCCGTATACGTTTCTAATTTGTAGTTAACGGTTGGATACCACTTTGAGG
+>12
+ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
+>13
+ACTGGATGCATCTGCAGGATATCGCGGCCGCAGAAGACCTAAGCTAGCGTTTAGAGTGCA
+>14
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>15
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>16
+CAAGCAGAAGACGGCATACGAGAT
+>17
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+>18
+GGGCCATACTAGTACTGGATGCATCTGCAGGATATCGCGGCCGCGTCTTCAGAGGGGGAT
+>19
+TGCACTCTAAACGCTAGCTTAGGTCTTCTGCGGCCGCGATATCCTGCAGATGCATCCAGT
+>20
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>21
+TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>22
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>23
+GTTGTGCAGAACCCTTGGAGTCTCATGGAATCGCGAATGGTCTCTAGGATCCCCCGGGCC
+>24
+GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
+>25
+GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>26
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>27
+GGCCCGGGGGATCCTAGAGACCATTCGCGATTCCATGAGACTCCAAGGGTTCTGCACAAC
+>28
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC
+T
+>29
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>30
+CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>31
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
diff --git a/data/2024-04-30_bengtsson-palme/hv_clade_counts.tsv.gz b/data/2024-04-30_bengtsson-palme/hv_clade_counts.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/hv_hits_blast_paired.tsv.gz b/data/2024-04-30_bengtsson-palme/hv_hits_blast_paired.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/hv_hits_putative_filtered.tsv.gz b/data/2024-04-30_bengtsson-palme/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/kraken_reports.tsv.gz b/data/2024-04-30_bengtsson-palme/kraken_reports.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/qc_adapter_stats.tsv.gz b/data/2024-04-30_bengtsson-palme/qc_adapter_stats.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/qc_basic_stats.tsv.gz b/data/2024-04-30_bengtsson-palme/qc_basic_stats.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/qc_quality_base_stats.tsv.gz b/data/2024-04-30_bengtsson-palme/qc_quality_base_stats.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/qc_quality_sequence_stats.tsv.gz b/data/2024-04-30_bengtsson-palme/qc_quality_sequence_stats.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/sample-metadata.csv b/data/2024-04-30_bengtsson-palme/sample-metadata.csv
@@ -0,0 +1,71 @@
+library,sample,location,sample_type,sample_alias,bioproject,dataset
+ERR1414209,ERR1414209,Uppsala,Primary/Surplus,102,PRJEB14051,Bengtsson-Palme 2016
+ERR1414210,ERR1414210,Uppsala,Primary/Surplus,103,PRJEB14051,Bengtsson-Palme 2016
+ERR1414211,ERR1414211,Uppsala,Primary/Surplus,104,PRJEB14051,Bengtsson-Palme 2016
+ERR1414212,ERR1414212,Uppsala,Surplus,105,PRJEB14051,Bengtsson-Palme 2016
+ERR1414213,ERR1414213,Uppsala,Surplus,106,PRJEB14051,Bengtsson-Palme 2016
+ERR1414214,ERR1414214,Uppsala,Surplus,107,PRJEB14051,Bengtsson-Palme 2016
+ERR1414215,ERR1414215,Uppsala,Surplus,108,PRJEB14051,Bengtsson-Palme 2016
+ERR1414216,ERR1414216,Uppsala,Digested,109,PRJEB14051,Bengtsson-Palme 2016
+ERR1414217,ERR1414217,Uppsala,Digested,110,PRJEB14051,Bengtsson-Palme 2016
+ERR1414218,ERR1414218,Uppsala,Digested,111,PRJEB14051,Bengtsson-Palme 2016
+ERR1414219,ERR1414219,Uppsala,Digested,112,PRJEB14051,Bengtsson-Palme 2016
+ERR1414220,ERR1414220,Käppala,Digested,113,PRJEB14051,Bengtsson-Palme 2016
+ERR1414221,ERR1414221,Käppala,Digested,114,PRJEB14051,Bengtsson-Palme 2016
+ERR1414222,ERR1414222,Käppala,Digested,115,PRJEB14051,Bengtsson-Palme 2016
+ERR1414223,ERR1414223,Käppala,Kemikond,117,PRJEB14051,Bengtsson-Palme 2016
+ERR1414224,ERR1414224,Käppala,Kemikond,118,PRJEB14051,Bengtsson-Palme 2016
+ERR1414225,ERR1414225,Käppala,Kemikond,119,PRJEB14051,Bengtsson-Palme 2016
+ERR1414226,ERR1414226,Käppala,Surplus,121,PRJEB14051,Bengtsson-Palme 2016
+ERR1414227,ERR1414227,Käppala,Surplus,122,PRJEB14051,Bengtsson-Palme 2016
+ERR1414228,ERR1414228,Käppala,Surplus,123,PRJEB14051,Bengtsson-Palme 2016
+ERR1414229,ERR1414229,Käppala,Surplus,124,PRJEB14051,Bengtsson-Palme 2016
+ERR1414230,ERR1414230,Henriksdal,Surplus,129,PRJEB14051,Bengtsson-Palme 2016
+ERR1414231,ERR1414231,Henriksdal,Surplus,130,PRJEB14051,Bengtsson-Palme 2016
+ERR1414232,ERR1414232,Henriksdal,Surplus,131,PRJEB14051,Bengtsson-Palme 2016
+ERR1414233,ERR1414233,Henriksdal,Digested,137,PRJEB14051,Bengtsson-Palme 2016
+ERR1414234,ERR1414234,Henriksdal,Digested,138,PRJEB14051,Bengtsson-Palme 2016
+ERR1414235,ERR1414235,Henriksdal,Digested,139,PRJEB14051,Bengtsson-Palme 2016
+ERR1414236,ERR1414236,Henriksdal,Digested,140,PRJEB14051,Bengtsson-Palme 2016
+ERR1414237,ERR1414237,Henriksdal,Inlet-HA,141,PRJEB14051,Bengtsson-Palme 2016
+ERR1414238,ERR1414238,Henriksdal,Inlet-HA,142,PRJEB14051,Bengtsson-Palme 2016
+ERR1414239,ERR1414239,Uppsala,Inlet-AD,143,PRJEB14051,Bengtsson-Palme 2016
+ERR1414240,ERR1414240,Uppsala,Inlet-AD,144,PRJEB14051,Bengtsson-Palme 2016
+ERR1414241,ERR1414241,Uppsala,Inlet-C,145,PRJEB14051,Bengtsson-Palme 2016
+ERR1414242,ERR1414242,Uppsala,Inlet-C,146,PRJEB14051,Bengtsson-Palme 2016
+ERR1414243,ERR1414243,Käppala,Inlet,147,PRJEB14051,Bengtsson-Palme 2016
+ERR1414244,ERR1414244,Käppala,Inlet,148,PRJEB14051,Bengtsson-Palme 2016
+ERR1414245,ERR1414245,Henriksdal,Inlet-S,149,PRJEB14051,Bengtsson-Palme 2016
+ERR1414246,ERR1414246,Henriksdal,Inlet-S,150,PRJEB14051,Bengtsson-Palme 2016
+ERR1414247,ERR1414247,Henriksdal,Inlet-Hab,151,PRJEB14051,Bengtsson-Palme 2016
+ERR1414248,ERR1414248,Henriksdal,Inlet-Hab,152,PRJEB14051,Bengtsson-Palme 2016
+ERR1414249,ERR1414249,Uppsala,Inlet-Adb,153,PRJEB14051,Bengtsson-Palme 2016
+ERR1414250,ERR1414250,Uppsala,Inlet-Adb,154,PRJEB14051,Bengtsson-Palme 2016
+ERR1414251,ERR1414251,Uppsala,Inlet-Cb,155,PRJEB14051,Bengtsson-Palme 2016
+ERR1414252,ERR1414252,Uppsala,Inlet-Cb,156,PRJEB14051,Bengtsson-Palme 2016
+ERR1414253,ERR1414253,Käppala,Inlet-b,157,PRJEB14051,Bengtsson-Palme 2016
+ERR1414254,ERR1414254,Käppala,Inlet-b,158,PRJEB14051,Bengtsson-Palme 2016
+ERR1414255,ERR1414255,Henriksdal,Inlet-Sb,159,PRJEB14051,Bengtsson-Palme 2016
+ERR1414256,ERR1414256,Henriksdal,Inlet-Sb,160,PRJEB14051,Bengtsson-Palme 2016
+ERR1414257,ERR1414257,Henriksdal,Treated,161,PRJEB14051,Bengtsson-Palme 2016
+ERR1414258,ERR1414258,Henriksdal,Treated,162,PRJEB14051,Bengtsson-Palme 2016
+ERR1414259,ERR1414259,Henriksdal,Sand-filtered,163,PRJEB14051,Bengtsson-Palme 2016
+ERR1414260,ERR1414260,Henriksdal,Sand-filtered,164,PRJEB14051,Bengtsson-Palme 2016
+ERR1414261,ERR1414261,Käppala,Treated,165,PRJEB14051,Bengtsson-Palme 2016
+ERR1414262,ERR1414262,Käppala,Treated,166,PRJEB14051,Bengtsson-Palme 2016
+ERR1414263,ERR1414263,Käppala,Sand-filtered,167,PRJEB14051,Bengtsson-Palme 2016
+ERR1414264,ERR1414264,Käppala,Sand-filtered,168,PRJEB14051,Bengtsson-Palme 2016
+ERR1414265,ERR1414265,Uppsala,Treated,169,PRJEB14051,Bengtsson-Palme 2016
+ERR1414266,ERR1414266,Uppsala,Treated,170,PRJEB14051,Bengtsson-Palme 2016
+ERR1414267,ERR1414267,Uppsala,Primary/Surplus,201,PRJEB14051,Bengtsson-Palme 2016
+ERR1414268,ERR1414268,Käppala,Digested,216,PRJEB14051,Bengtsson-Palme 2016
+ERR1414269,ERR1414269,Käppala,Kemikond,220,PRJEB14051,Bengtsson-Palme 2016
+ERR1414270,ERR1414270,Käppala,Primary,225,PRJEB14051,Bengtsson-Palme 2016
+ERR1414271,ERR1414271,Käppala,Primary,226,PRJEB14051,Bengtsson-Palme 2016
+ERR1414272,ERR1414272,Käppala,Primary,227,PRJEB14051,Bengtsson-Palme 2016
+ERR1414273,ERR1414273,Käppala,Primary,228,PRJEB14051,Bengtsson-Palme 2016
+ERR1414274,ERR1414274,Henriksdal,Surplus,232,PRJEB14051,Bengtsson-Palme 2016
+ERR1414275,ERR1414275,Henriksdal,Primary,233,PRJEB14051,Bengtsson-Palme 2016
+ERR1414276,ERR1414276,Henriksdal,Primary,234,PRJEB14051,Bengtsson-Palme 2016
+ERR1414277,ERR1414277,Henriksdal,Primary,235,PRJEB14051,Bengtsson-Palme 2016
+ERR1414278,ERR1414278,Henriksdal,Primary,236,PRJEB14051,Bengtsson-Palme 2016
diff --git a/data/2024-04-30_bengtsson-palme/take2/hv_hits_blast_paired.tsv.gz b/data/2024-04-30_bengtsson-palme/take2/hv_hits_blast_paired.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/take2/hv_hits_putative_filtered.tsv.gz b/data/2024-04-30_bengtsson-palme/take2/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/taxid-names.tsv.gz b/data/2024-04-30_bengtsson-palme/taxid-names.tsv.gz
@@ -0,0 +1 @@
+../2024-04-01_spurbeck/taxid-names.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/taxonomic_composition.tsv.gz b/data/2024-04-30_bengtsson-palme/taxonomic_composition.tsv.gz
diff --git a/data/2024-04-30_bengtsson-palme/viral-taxids.tsv.gz b/data/2024-04-30_bengtsson-palme/viral-taxids.tsv.gz
@@ -0,0 +1 @@
+../2024-03-19_brumfield/viral-taxids.tsv.gz