-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathcontaminome.yml
210 lines (210 loc) · 8.63 KB
/
contaminome.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
eukaryotes:
Homo Sapiens:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna.gz
vulgarname: human
accession: GCF_000001405.40
taxid: 9606
Mus musculus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.fna.gz
vulgarname: mouse
accession: GCF_000001635.27
taxid: 10090
Drosophila melanogaster:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz
vulgarname: fly
accession: GCF_000001215.4
taxid: 7227
Aedes aegypti:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/204/515/GCF_002204515.2_AaegL5.0/GCF_002204515.2_AaegL5.0_genomic.fna.gz
vulgarname: aedes-aegypti
accession: GCF_002204515.2
taxid: 7159
Petromyzon marinus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/993/605/GCF_010993605.1_kPetMar1.pri/GCF_010993605.1_kPetMar1.pri_genomic.fna.gz
vulgarname: sea-lamprey
accession: GCF_010993605.1
taxid: 7757
Oryzias latipes:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/234/675/GCF_002234675.1_ASM223467v1/GCF_002234675.1_ASM223467v1_genomic.fna.gz
vulgarname: japanese-medaka
accession: GCF_002234675.1
taxid: 8090
Caenorhabditis elegans:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.fna.gz
vulgarname: c-elegans
accession: GCF_000002985.6
taxid: 6239
Saccharomyces cerevisiae:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz
vulgarname: yeast
accession: GCF_000146045.2
taxid: 4932
Schizosaccharomyces pombe:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/945/GCF_000002945.2_ASM294v3/GCF_000002945.2_ASM294v3_genomic.fna.gz
vulgarname: fission-yeast
accession: GCF_000002945.2
taxid: 4896
Danio rerio:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.6_GRCz11/GCF_000002035.6_GRCz11_genomic.fna.gz
vulgarname: zebrafish
accession: GCF_000002035.6
taxid: 7955
Hypsibius dujardini:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/579/985/GCA_001579985.1_ASM157998v1/GCA_001579985.1_ASM157998v1_genomic.fna.gz
vulgarname: moss-piglet
accession: GCA_001579985.1
taxid: 232323
prokaryotes:
Escherichia coli:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
vulgarname: ecoli
accession: GCF_000005845.2
taxid: 562
Pseudomonas aeruginosa:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/765/GCF_000006765.1_ASM676v1/GCF_000006765.1_ASM676v1_genomic.fna.gz
vulgarname: pseudomonas-aeruginosa
accession: GCF_000006765.1
taxid: 287
Pseudomonas putidia:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/412/675/GCF_000412675.1_ASM41267v1/GCF_000412675.1_ASM41267v1_genomic.fna.gz
vulgarname: pseudomonas-putidia
accession: GCF_000412675.1
taxid: 1211579
Pseudomonas fulva:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/186/195/GCF_001186195.1_ASM118619v1/GCF_001186195.1_ASM118619v1_genomic.fna.gz
vulgarname: pseudomonas-fulva
accession: GCF_001186195.1
taxid: 47880
Acholeplasma laidlawii:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/385/765/GCF_003385765.1_ASM338576v1/GCF_003385765.1_ASM338576v1_genomic.fna.gz
vulgarname: mycoplasma
accession: GCF_003385765.1
taxid: 2148
Mesomycoplasma hyorhinis:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/383/515/GCF_000383515.1_ASM38351v1/GCF_000383515.1_ASM38351v1_genomic.fna.gz
vulgarname: mycoplasma-hyorhinis
accession: GCF000383515.1
taxid: 2100
Haemophilus influenzae:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/931/575/GCF_000931575.1_ASM93157v1/GCF_000931575.1_ASM93157v1_genomic.fna.gz
vulgarname: haemophilus
accession: GCF_000931575.1
taxid: 727
Wolbachia melanogaster symbiont:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/584/425/GCA_016584425.1_ASM1658442v1/GCA_016584425.1_ASM1658442v1_genomic.fna.gz
vulgarname: wolbachia
accession: GCF_016584425.1
taxid: 163164
Staphylococcus aureus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz
vulgarname: staph_aureus
accession: GCF_000013425.1
taxid: 1280
custom:
Severe acute respiratory syndrome coronavirus 2:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz
vulgarname: sars-cov2
accession: GCF_009858895.2
taxid: 2697049
Influenza A:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/865/085/GCF_000865085.1_ViralMultiSegProj15622/GCF_000865085.1_ViralMultiSegProj15622_genomic.fna.gz
vulgarname: flu-a
accession: GCF_000865085.1
taxid: 335341
Norwalk virus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/864/005/GCF_000864005.1_ViralProj15520/GCF_000864005.1_ViralProj15520_genomic.fna.gz
vulgarname: noro
accession: GCF_000864005.1
taxid: 11983
Influenza B:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/influenzab.fna.gz
vulgarname: flu-b
accession: NC_002211.1
taxid: 11520
Rhinovirus A:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/rhinoa.fna.gz
vulgarname: common-cold-a
accession: NC_038311.1
taxid: 573824
Rhinovirus B:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/rhinob.fna.gz
vulgarname: common-cold-b
accession: NC_001490.1
taxid: 12131
Drosophila C virus:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/drosophilac.fna.gz
vulgarname: drosophila-c-virus
accession: NC_001834.1
taxid: 64279
Escherichia phage phiX174:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/phix.fna.gz
vulgarname: phix
accession: NC_001422.1
taxid: 2886930
Enterobacteria phage lambda:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/lambdaphage.fna.gz
vulgarname: lambdaphage
accession: NC_001416.1
taxid: 10710
UniVec_core:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/univec_core.fna.gz
vulgarname: vectors
accession: NA
taxid: 29278
ERCC:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/ercc.fna.gz
vulgarname: ercc
accession: NA
taxid: 292781111
rrna:
Homo sapiens pre-rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/human45s.fna.gz
vulgarname: humanrrna
accession: NR_046235.3
taxid: 96061111
Mus musculus pre-rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/mouse45s.fna.gz
vulgarname: mouserrna
accession: NR_046233.2
taxid: 100901111
Drosophila melanogaster pre-rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/fly45s.fna.gz
vulgarname: flyrrna
accession: NR_133549.1
taxid: 72271111
Aedes aegypti 28SrRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/aedesaegypti28s.fna.gz
vulgarname: aedesaegyptirrna
accession: NC_035159.1
taxid: 71591111
Zebrafish rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/zebrarRNA.fna.gz
vulgarname: zebrafishrrna
accession: NR_145818.1
taxid: 79551111
mito:
Homo sapiens mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/humanmito.fna.gz
vulgarname: humanmito
accession: NC_012920.1
taxid: 96062222
Mus musculus mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/mousemito.fna.gz
vulgarname: mousemito
accession: NC_005089.1
taxid: 100902222
Drosophila melanogaster mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/flymito.fna.gz
vulgarname: flymito
accession: NC_024511.2
taxid: 72272222
Aedes aegypti mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/aedesaegyptimito.fna.gz
vulgarname: aedesaegyptimito
accession: NC_035159.1
taxid: 71592222
Zebrafish mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/zebramito.fna.gz
vulgarname: zebrafishmito
accession: NC_002333.2
taxid: 79552222