Added Rosario analysis

naobservatory · Apr 12, 2024 · 70c1a9a · 70c1a9a
1 parent d496c27
commit 70c1a9a
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Showing 78 changed files with 38,534 additions and 9 deletions.
diff --git a/data/2024-04-12_rosario/adapters.fasta b/data/2024-04-12_rosario/adapters.fasta
@@ -0,0 +1,41 @@
+>0
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC
+>1
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>2
+heifigepsna
+>3
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC
+T
+>4
+GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>5
+CAAGCAGAAGACGGCATACGAGAT
+>6
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>7
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>8
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>9
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>10
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+>11
+CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>12
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>13
+TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>14
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>15
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>16
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+>17
+unspecified
+>18
+GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>19
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
diff --git a/data/2024-04-12_rosario/blast/putative-viral.blast.gz b/data/2024-04-12_rosario/blast/putative-viral.blast.gz
diff --git a/data/2024-04-12_rosario/bracken_counts.tsv b/data/2024-04-12_rosario/bracken_counts.tsv
@@ -0,0 +1,105 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads	sample
+Bacteria	2	D	52692	6	52698	0.65873	SRR5853131
+Eukaryota	2759	D	27206	26	27232	0.3404	SRR5853131
+Archaea	2157	D	32	0	32	4e-4	SRR5853131
+Viruses	10239	D	37	0	37	4.6e-4	SRR5853131
+Bacteria	2	D	13591	7	13598	0.64762	SRR5853127
+Eukaryota	2759	D	7311	14	7325	0.34886	SRR5853127
+Archaea	2157	D	30	0	30	0.00143	SRR5853127
+Viruses	10239	D	43	0	43	0.00205	SRR5853127
+Eukaryota	2759	D	33058	34	33092	0.6138	SRR5853125
+Bacteria	2	D	20641	5	20646	0.38295	SRR5853125
+Archaea	2157	D	73	0	73	0.00135	SRR5853125
+Viruses	10239	D	100	0	100	0.00185	SRR5853125
+Eukaryota	2759	D	98064	35	98099	0.746	SRR5853144
+Bacteria	2	D	33145	26	33171	0.25225	SRR5853144
+Archaea	2157	D	8	0	8	6e-5	SRR5853144
+Viruses	10239	D	212	9	221	0.00168	SRR5853144
+Eukaryota	2759	D	145136	61	145197	0.76421	SRR5853124
+Bacteria	2	D	44403	18	44421	0.2338	SRR5853124
+Archaea	2157	D	62	0	62	3.3e-4	SRR5853124
+Viruses	10239	D	312	1	313	0.00165	SRR5853124
+Eukaryota	2759	D	123970	53	124023	0.70438	SRR5853147
+Bacteria	2	D	51636	56	51692	0.29358	SRR5853147
+Archaea	2157	D	17	0	17	1e-4	SRR5853147
+Viruses	10239	D	336	3	339	0.00193	SRR5853147
+Bacteria	2	D	15818	5	15823	0.59809	SRR5853123
+Eukaryota	2759	D	10505	18	10523	0.39775	SRR5853123
+Archaea	2157	D	54	0	54	0.00204	SRR5853123
+Viruses	10239	D	55	0	55	0.00208	SRR5853123
+Eukaryota	2759	D	171880	52	171932	0.85984	SRR5853132
+Bacteria	2	D	27277	32	27309	0.13657	SRR5853132
+Archaea	2157	D	9	0	9	5e-5	SRR5853132
+Viruses	10239	D	706	0	706	0.00353	SRR5853132
+Bacteria	2	D	23143	8	23151	0.69873	SRR5853128
+Eukaryota	2759	D	9802	26	9828	0.29662	SRR5853128
+Archaea	2157	D	59	0	59	0.00178	SRR5853128
+Viruses	10239	D	93	0	93	0.00281	SRR5853128
+Eukaryota	2759	D	42760	30	42790	0.60158	SRR5853148
+Bacteria	2	D	28069	30	28099	0.39504	SRR5853148
+Archaea	2157	D	5	0	5	7e-5	SRR5853148
+Viruses	10239	D	230	3	233	0.00328	SRR5853148
+Eukaryota	2759	D	96400	54	96454	0.79326	SRR5853145
+Bacteria	2	D	25034	22	25056	0.20607	SRR5853145
+Archaea	2157	D	13	0	13	1.1e-4	SRR5853145
+Viruses	10239	D	67	1	68	5.6e-4	SRR5853145
+Eukaryota	2759	D	68344	49	68393	0.57312	SRR5853140
+Bacteria	2	D	48742	46	48788	0.40884	SRR5853140
+Archaea	2157	D	9	0	9	8e-5	SRR5853140
+Viruses	10239	D	2135	7	2142	0.01795	SRR5853140
+Eukaryota	2759	D	36882	33	36915	0.52574	SRR5853137
+Bacteria	2	D	32757	16	32773	0.46675	SRR5853137
+Archaea	2157	D	60	0	60	8.5e-4	SRR5853137
+Viruses	10239	D	465	0	465	0.00662	SRR5853137
+Eukaryota	2759	D	39600	93	39693	0.59161	SRR5853133
+Bacteria	2	D	26270	94	26364	0.39295	SRR5853133
+Archaea	2157	D	16	0	16	2.4e-4	SRR5853133
+Viruses	10239	D	1006	12	1018	0.01517	SRR5853133
+Bacteria	2	D	27595	39	27634	0.76455	SRR5853139
+Eukaryota	2759	D	7963	23	7986	0.22095	SRR5853139
+Archaea	2157	D	64	0	64	0.00177	SRR5853139
+Viruses	10239	D	428	31	459	0.0127	SRR5853139
+Eukaryota	2759	D	24667	28	24695	0.56764	SRR5853122
+Bacteria	2	D	18591	11	18602	0.42758	SRR5853122
+Archaea	2157	D	46	0	46	0.00106	SRR5853122
+Viruses	10239	D	159	1	160	0.00368	SRR5853122
+Eukaryota	2759	D	60858	48	60906	0.60764	SRR5853146
+Bacteria	2	D	36346	33	36379	0.36294	SRR5853146
+Archaea	2157	D	113	0	113	0.00113	SRR5853146
+Viruses	10239	D	2832	1	2833	0.02826	SRR5853146
+Eukaryota	2759	D	69012	42	69054	0.59244	SRR5853141
+Bacteria	2	D	47146	31	47177	0.40475	SRR5853141
+Archaea	2157	D	9	0	9	8e-5	SRR5853141
+Viruses	10239	D	316	1	317	0.00272	SRR5853141
+Bacteria	2	D	19442	9	19451	0.51556	SRR5853129
+Eukaryota	2759	D	18090	30	18120	0.48028	SRR5853129
+Archaea	2157	D	39	0	39	0.00103	SRR5853129
+Viruses	10239	D	117	0	117	0.0031	SRR5853129
+Eukaryota	2759	D	615098	205	615303	0.99542	SRR5853149
+Bacteria	2	D	2813	0	2813	0.00455	SRR5853149
+Archaea	2157	D	2	0	2	0	SRR5853149
+Viruses	10239	D	12	0	12	2e-5	SRR5853149
+Eukaryota	2759	D	27478	30	27508	0.52723	SRR5853130
+Bacteria	2	D	24327	19	24346	0.46662	SRR5853130
+Archaea	2157	D	52	0	52	0.001	SRR5853130
+Viruses	10239	D	261	6	267	0.00512	SRR5853130
+Bacteria	2	D	25695	37	25732	0.83749	SRR5853138
+Eukaryota	2759	D	4658	25	4683	0.15242	SRR5853138
+Archaea	2157	D	72	0	72	0.00234	SRR5853138
+Viruses	10239	D	230	7	237	0.00771	SRR5853138
+Bacteria	2	D	42731	29	42760	0.63481	SRR5853136
+Eukaryota	2759	D	23253	44	23297	0.34586	SRR5853136
+Archaea	2157	D	90	0	90	0.00134	SRR5853136
+Viruses	10239	D	1200	10	1210	0.01796	SRR5853136
+Eukaryota	2759	D	205366	53	205419	0.82829	SRR5853143
+Bacteria	2	D	42307	22	42329	0.17068	SRR5853143
+Archaea	2157	D	17	0	17	7e-5	SRR5853143
+Viruses	10239	D	239	0	239	9.6e-4	SRR5853143
+Eukaryota	2759	D	41496	22	41518	0.81962	SRR5853134
+Bacteria	2	D	8656	66	8722	0.17218	SRR5853134
+Archaea	2157	D	2	0	2	4e-5	SRR5853134
+Viruses	10239	D	411	0	411	0.00811	SRR5853134
+Eukaryota	2759	D	49882	35	49917	0.81505	SRR5853135
+Bacteria	2	D	11210	69	11279	0.18416	SRR5853135
+Archaea	2157	D	7	0	7	1.1e-4	SRR5853135
+Viruses	10239	D	40	0	40	6.5e-4	SRR5853135
diff --git a/data/2024-04-12_rosario/hv_clade_counts.tsv.gz b/data/2024-04-12_rosario/hv_clade_counts.tsv.gz
diff --git a/data/2024-04-12_rosario/hv_hits_putative_filtered.tsv.gz b/data/2024-04-12_rosario/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853122.report.gz b/data/2024-04-12_rosario/kraken/SRR5853122.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853123.report.gz b/data/2024-04-12_rosario/kraken/SRR5853123.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853124.report.gz b/data/2024-04-12_rosario/kraken/SRR5853124.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853125.report.gz b/data/2024-04-12_rosario/kraken/SRR5853125.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853127.report.gz b/data/2024-04-12_rosario/kraken/SRR5853127.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853128.report.gz b/data/2024-04-12_rosario/kraken/SRR5853128.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853129.report.gz b/data/2024-04-12_rosario/kraken/SRR5853129.report.gz
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diff --git a/data/2024-04-12_rosario/kraken/SRR5853132.report.gz b/data/2024-04-12_rosario/kraken/SRR5853132.report.gz
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diff --git a/data/2024-04-12_rosario/kraken/SRR5853134.report.gz b/data/2024-04-12_rosario/kraken/SRR5853134.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853135.report.gz b/data/2024-04-12_rosario/kraken/SRR5853135.report.gz
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diff --git a/data/2024-04-12_rosario/kraken/SRR5853140.report.gz b/data/2024-04-12_rosario/kraken/SRR5853140.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853141.report.gz b/data/2024-04-12_rosario/kraken/SRR5853141.report.gz
diff --git a/data/2024-04-12_rosario/kraken/SRR5853143.report.gz b/data/2024-04-12_rosario/kraken/SRR5853143.report.gz
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