Added Prussin analysis

naobservatory · Apr 12, 2024 · bdf0957 · bdf0957
1 parent 59857db
commit bdf0957
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Showing 113 changed files with 55,687 additions and 482 deletions.
diff --git a/data/2024-04-11_prussin/adapters.fasta b/data/2024-04-11_prussin/adapters.fasta
@@ -0,0 +1,45 @@
+>0
+CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+>1
+GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+>2
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>3
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+>4
+CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+>5
+GGCTCAAACCATGCACCGAAGCTACGGGTATCATCTTTTGATGATGCGGTAGAGGAGCGT
+>6
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>7
+ACGCTCCTCTACCGCATCATCAAAAGATGATACCCGTAGCTTCGGTGCATGGTTTGAGCC
+>8
+heifigepsna
+>9
+unspecified
+>10
+TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+>11
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>12
+CAAGCAGAAGACGGCATACGAGAT
+>13
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+>14
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>15
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC
+>16
+ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>17
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>18
+GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+>19
+CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC
+T
+>20
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+>21
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
diff --git a/data/2024-04-11_prussin/blast/putative-viral-best.blast.gz b/data/2024-04-11_prussin/blast/putative-viral-best.blast.gz
diff --git a/data/2024-04-11_prussin/bracken_counts.tsv b/data/2024-04-11_prussin/bracken_counts.tsv
@@ -0,0 +1,129 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads	sample
+Eukaryota	2759	D	23114	29	23143	0.76011	SRR8663608
+Bacteria	2	D	6306	12	6318	0.20751	SRR8663608
+Archaea	2157	D	10	0	10	3.3e-4	SRR8663608
+Viruses	10239	D	975	0	975	0.03202	SRR8663608
+Bacteria	2	D	4858723	155	4858878	0.96863	SRR8663601
+Eukaryota	2759	D	157096	50	157146	0.03133	SRR8663601
+Archaea	2157	D	114	0	114	2e-5	SRR8663601
+Viruses	10239	D	112	0	112	2e-5	SRR8663601
+Eukaryota	2759	D	2020112	2501	2022613	0.87927	SRR8663623
+Bacteria	2	D	273553	521	274074	0.11915	SRR8663623
+Archaea	2157	D	998	0	998	4.3e-4	SRR8663623
+Viruses	10239	D	2608	25	2633	0.00114	SRR8663623
+Eukaryota	2759	D	12876337	8753	12885090	0.77634	SRR8663617
+Bacteria	2	D	3697581	2422	3700003	0.22293	SRR8663617
+Archaea	2157	D	6559	0	6559	4e-4	SRR8663617
+Viruses	10239	D	5444	89	5533	3.3e-4	SRR8663617
+Eukaryota	2759	D	15931509	12059	15943568	0.7655	SRR8663615
+Bacteria	2	D	4869174	3112	4872286	0.23393	SRR8663615
+Archaea	2157	D	6713	0	6713	3.2e-4	SRR8663615
+Viruses	10239	D	4982	125	5107	2.5e-4	SRR8663615
+Eukaryota	2759	D	2618585	2592	2621177	0.89805	SRR8663620
+Bacteria	2	D	291171	495	291666	0.09993	SRR8663620
+Archaea	2157	D	1103	0	1103	3.8e-4	SRR8663620
+Viruses	10239	D	4789	12	4801	0.00164	SRR8663620
+Eukaryota	2759	D	3179073	2287	3181360	0.63287	SRR8663619
+Bacteria	2	D	1841428	704	1842132	0.36646	SRR8663619
+Archaea	2157	D	1455	0	1455	2.9e-4	SRR8663619
+Viruses	10239	D	1888	15	1903	3.8e-4	SRR8663619
+Eukaryota	2759	D	2131400	2592	2133992	0.89031	SRR8663622
+Bacteria	2	D	258666	380	259046	0.10808	SRR8663622
+Archaea	2157	D	935	0	935	3.9e-4	SRR8663622
+Viruses	10239	D	2891	31	2922	0.00122	SRR8663622
+Eukaryota	2759	D	4468846	2761	4471607	0.90883	SRR8663627
+Bacteria	2	D	443530	658	444188	0.09028	SRR8663627
+Archaea	2157	D	1505	0	1505	3.1e-4	SRR8663627
+Viruses	10239	D	2842	21	2863	5.8e-4	SRR8663627
+Bacteria	2	D	6453514	198	6453712	0.9413	SRR8663600
+Eukaryota	2759	D	402127	104	402231	0.05867	SRR8663600
+Archaea	2157	D	148	0	148	2e-5	SRR8663600
+Viruses	10239	D	83	0	83	1e-5	SRR8663600
+Eukaryota	2759	D	6950380	4713	6955093	0.76802	SRR8663604
+Bacteria	2	D	2094895	1301	2096196	0.23147	SRR8663604
+Archaea	2157	D	2294	0	2294	2.5e-4	SRR8663604
+Viruses	10239	D	2212	48	2260	2.5e-4	SRR8663604
+Eukaryota	2759	D	2315070	2745	2317815	0.89866	SRR8663621
+Bacteria	2	D	256987	430	257417	0.09981	SRR8663621
+Archaea	2157	D	911	0	911	3.5e-4	SRR8663621
+Viruses	10239	D	3036	9	3045	0.00118	SRR8663621
+Eukaryota	2759	D	4329068	3381	4332449	0.65941	SRR8663610
+Bacteria	2	D	2230419	1179	2231598	0.33966	SRR8663610
+Archaea	2157	D	1934	0	1934	2.9e-4	SRR8663610
+Viruses	10239	D	4139	25	4164	6.3e-4	SRR8663610
+Eukaryota	2759	D	6715965	5636	6721601	0.66434	SRR8663605
+Bacteria	2	D	3387664	2144	3389808	0.33504	SRR8663605
+Archaea	2157	D	2830	0	2830	2.8e-4	SRR8663605
+Viruses	10239	D	3439	38	3477	3.4e-4	SRR8663605
+Bacteria	2	D	4804040	1353	4805393	0.71165	SRR8663606
+Eukaryota	2759	D	1939671	2381	1942052	0.28761	SRR8663606
+Archaea	2157	D	2418	0	2418	3.6e-4	SRR8663606
+Viruses	10239	D	2596	11	2607	3.9e-4	SRR8663606
+Eukaryota	2759	D	5797094	4420	5801514	0.70566	SRR8663613
+Bacteria	2	D	2412241	1172	2413413	0.29355	SRR8663613
+Archaea	2157	D	2612	0	2612	3.2e-4	SRR8663613
+Viruses	10239	D	3841	28	3869	4.7e-4	SRR8663613
+Eukaryota	2759	D	14475	19	14494	0.66925	SRR8663609
+Bacteria	2	D	6474	11	6485	0.29944	SRR8663609
+Archaea	2157	D	5	0	5	2.3e-4	SRR8663609
+Viruses	10239	D	672	0	672	0.03103	SRR8663609
+Eukaryota	2759	D	3261369	2536	3263905	0.90304	SRR8663628
+Bacteria	2	D	346222	544	346766	0.09594	SRR8663628
+Archaea	2157	D	1554	0	1554	4.3e-4	SRR8663628
+Viruses	10239	D	2098	28	2126	5.9e-4	SRR8663628
+Eukaryota	2759	D	3890470	3542	3894012	0.88618	SRR8663598
+Bacteria	2	D	488469	681	489150	0.11132	SRR8663598
+Archaea	2157	D	1902	0	1902	4.3e-4	SRR8663598
+Viruses	10239	D	9058	17	9075	0.00207	SRR8663598
+Eukaryota	2759	D	4554828	3549	4558377	0.71166	SRR8663611
+Bacteria	2	D	1841167	959	1842126	0.28759	SRR8663611
+Archaea	2157	D	1958	0	1958	3.1e-4	SRR8663611
+Viruses	10239	D	2794	51	2845	4.4e-4	SRR8663611
+Eukaryota	2759	D	740508	709	741217	0.65795	SRR8663629
+Bacteria	2	D	383307	272	383579	0.34049	SRR8663629
+Archaea	2157	D	699	0	699	6.2e-4	SRR8663629
+Viruses	10239	D	1056	2	1058	9.4e-4	SRR8663629
+Eukaryota	2759	D	4082341	2951	4085292	0.68913	SRR8663614
+Bacteria	2	D	1838109	784	1838893	0.3102	SRR8663614
+Archaea	2157	D	2149	0	2149	3.6e-4	SRR8663614
+Viruses	10239	D	1795	16	1811	3.1e-4	SRR8663614
+Eukaryota	2759	D	2354891	2349	2357240	0.86425	SRR8663626
+Bacteria	2	D	363337	580	363917	0.13343	SRR8663626
+Archaea	2157	D	906	0	906	3.3e-4	SRR8663626
+Viruses	10239	D	5413	9	5422	0.00199	SRR8663626
+Eukaryota	2759	D	6198690	3751	6202441	0.91084	SRR8663603
+Bacteria	2	D	599468	977	600445	0.08818	SRR8663603
+Archaea	2157	D	2598	0	2598	3.8e-4	SRR8663603
+Viruses	10239	D	4072	55	4127	6.1e-4	SRR8663603
+Eukaryota	2759	D	4519228	2808	4522036	0.90716	SRR8663599
+Bacteria	2	D	458033	691	458724	0.09202	SRR8663599
+Archaea	2157	D	1796	0	1796	3.6e-4	SRR8663599
+Viruses	10239	D	2264	28	2292	4.6e-4	SRR8663599
+Eukaryota	2759	D	6296110	5024	6301134	0.72846	SRR8663607
+Bacteria	2	D	2342386	1298	2343684	0.27095	SRR8663607
+Archaea	2157	D	3132	0	3132	3.6e-4	SRR8663607
+Viruses	10239	D	2002	31	2033	2.4e-4	SRR8663607
+Eukaryota	2759	D	4983881	3909	4987790	0.68704	SRR8663612
+Bacteria	2	D	2264835	1027	2265862	0.31211	SRR8663612
+Archaea	2157	D	2349	0	2349	3.2e-4	SRR8663612
+Viruses	10239	D	3767	20	3787	5.2e-4	SRR8663612
+Eukaryota	2759	D	1353957	1958	1355915	0.85703	SRR8663624
+Bacteria	2	D	221917	313	222230	0.14046	SRR8663624
+Archaea	2157	D	568	0	568	3.6e-4	SRR8663624
+Viruses	10239	D	3385	4	3389	0.00214	SRR8663624
+Eukaryota	2759	D	16240454	11556	16252010	0.77795	SRR8663616
+Bacteria	2	D	4622185	2974	4625159	0.2214	SRR8663616
+Archaea	2157	D	6551	0	6551	3.1e-4	SRR8663616
+Viruses	10239	D	7029	117	7146	3.4e-4	SRR8663616
+Eukaryota	2759	D	7994576	4641	7999217	0.91032	SRR8663602
+Bacteria	2	D	778005	1429	779434	0.0887	SRR8663602
+Archaea	2157	D	2960	0	2960	3.4e-4	SRR8663602
+Viruses	10239	D	5601	79	5680	6.5e-4	SRR8663602
+Eukaryota	2759	D	9282055	7402	9289457	0.63742	SRR8663618
+Bacteria	2	D	5270095	2864	5272959	0.36182	SRR8663618
+Archaea	2157	D	4454	0	4454	3.1e-4	SRR8663618
+Viruses	10239	D	6519	59	6578	4.5e-4	SRR8663618
+Eukaryota	2759	D	2074031	2319	2076350	0.86058	SRR8663625
+Bacteria	2	D	331748	444	332192	0.13768	SRR8663625
+Archaea	2157	D	869	0	869	3.6e-4	SRR8663625
+Viruses	10239	D	3315	11	3326	0.00138	SRR8663625
diff --git a/data/2024-04-11_prussin/hv_clade_counts.tsv.gz b/data/2024-04-11_prussin/hv_clade_counts.tsv.gz
diff --git a/data/2024-04-11_prussin/hv_hits_putative_filtered.tsv.gz b/data/2024-04-11_prussin/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-04-11_prussin/kraken/SRR8663598.report.gz b/data/2024-04-11_prussin/kraken/SRR8663598.report.gz
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