-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathconfig.yaml
502 lines (499 loc) · 29.2 KB
/
config.yaml
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
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
samples:
PNUSAC001306:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001306_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001306_2.fastq.gz
locustag: "PNUSAC001306"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001307:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001307_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001307_2.fastq.gz
locustag: "PNUSAC001307"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001308:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001308_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001308_2.fastq.gz
locustag: "PNUSAC001308"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001309:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001309_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001309_2.fastq.gz
locustag: "PNUSAC001309"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001310:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001310_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001310_2.fastq.gz
locustag: "PNUSAC001310"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001311:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001311_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001311_2.fastq.gz
locustag: "PNUSAC001311"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001312:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001312_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001312_2.fastq.gz
locustag: "PNUSAC001312"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001313:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001313_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001313_2.fastq.gz
locustag: "PNUSAC001313"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001314:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001314_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001314_2.fastq.gz
locustag: "PNUSAC001314"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001315:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001315_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001315_2.fastq.gz
locustag: "PNUSAC001315"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001316:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001316_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001316_2.fastq.gz
locustag: "PNUSAC001316"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001317:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001317_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001317_2.fastq.gz
locustag: "PNUSAC001317"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001318:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001318_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001318_2.fastq.gz
locustag: "PNUSAC001318"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001319:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001319_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001319_2.fastq.gz
locustag: "PNUSAC001319"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001320:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001320_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001320_2.fastq.gz
locustag: "PNUSAC001320"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001321:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001321_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001321_2.fastq.gz
locustag: "PNUSAC001321"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001322:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001322_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001322_2.fastq.gz
locustag: "PNUSAC001322"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001323:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001323_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001323_2.fastq.gz
locustag: "PNUSAC001323"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001325:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001325_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001325_2.fastq.gz
locustag: "PNUSAC001325"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001326:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001326_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001326_2.fastq.gz
locustag: "PNUSAC001326"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001327:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001327_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001327_2.fastq.gz
locustag: "PNUSAC001327"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001328:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001328_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001328_2.fastq.gz
locustag: "PNUSAC001328"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001329:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001329_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001329_2.fastq.gz
locustag: "PNUSAC001329"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001330:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001330_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001330_2.fastq.gz
locustag: "PNUSAC001330"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001331:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001331_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001331_2.fastq.gz
locustag: "PNUSAC001331"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001332:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001332_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001332_2.fastq.gz
locustag: "PNUSAC001332"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001333:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001333_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001333_2.fastq.gz
locustag: "PNUSAC001333"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001334:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001334_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001334_2.fastq.gz
locustag: "PNUSAC001334"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001335:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001335_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001335_2.fastq.gz
locustag: "PNUSAC001335"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001336:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001336_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001336_2.fastq.gz
locustag: "PNUSAC001336"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001337:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001337_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001337_2.fastq.gz
locustag: "PNUSAC001337"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001338:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001338_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001338_2.fastq.gz
locustag: "PNUSAC001338"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001339:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001339_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001339_2.fastq.gz
locustag: "PNUSAC001339"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001340:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001340_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001340_2.fastq.gz
locustag: "PNUSAC001340"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001341:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001341_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001341_2.fastq.gz
locustag: "PNUSAC001341"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001342:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001342_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001342_2.fastq.gz
locustag: "PNUSAC001342"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001343:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001343_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001343_2.fastq.gz
locustag: "PNUSAC001343"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001344:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001344_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001344_2.fastq.gz
locustag: "PNUSAC001344"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001345:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001345_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001345_2.fastq.gz
locustag: "PNUSAC001345"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001346:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001346_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001346_2.fastq.gz
locustag: "PNUSAC001346"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001347:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001347_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001347_2.fastq.gz
locustag: "PNUSAC001347"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001348:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001348_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001348_2.fastq.gz
locustag: "PNUSAC001348"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001349:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001349_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001349_2.fastq.gz
locustag: "PNUSAC001349"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001350:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001350_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001350_2.fastq.gz
locustag: "PNUSAC001350"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001351:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001351_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001351_2.fastq.gz
locustag: "PNUSAC001351"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001352:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001352_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001352_2.fastq.gz
locustag: "PNUSAC001352"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001353:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001353_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001353_2.fastq.gz
locustag: "PNUSAC001353"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001354:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001354_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001354_2.fastq.gz
locustag: "PNUSAC001354"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001355:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001355_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001355_2.fastq.gz
locustag: "PNUSAC001355"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001356:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001356_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001356_2.fastq.gz
locustag: "PNUSAC001356"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001357:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001357_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001357_2.fastq.gz
locustag: "PNUSAC001357"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001358:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001358_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001358_2.fastq.gz
locustag: "PNUSAC001358"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001359:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001359_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001359_2.fastq.gz
locustag: "PNUSAC001359"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001360:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001360_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001360_2.fastq.gz
locustag: "PNUSAC001360"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001361:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001361_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001361_2.fastq.gz
locustag: "PNUSAC001361"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001362:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001362_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001362_2.fastq.gz
locustag: "PNUSAC001362"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001363:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001363_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001363_2.fastq.gz
locustag: "PNUSAC001363"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001364:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001364_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001364_2.fastq.gz
locustag: "PNUSAC001364"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001365:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001365_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001365_2.fastq.gz
locustag: "PNUSAC001365"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001366:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001366_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001366_2.fastq.gz
locustag: "PNUSAC001366"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001367:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001367_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001367_2.fastq.gz
locustag: "PNUSAC001367"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001368:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001368_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001368_2.fastq.gz
locustag: "PNUSAC001368"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001369:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001369_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001369_2.fastq.gz
locustag: "PNUSAC001369"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001370:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001370_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001370_2.fastq.gz
locustag: "PNUSAC001370"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001371:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001371_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001371_2.fastq.gz
locustag: "PNUSAC001371"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001372:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001372_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001372_2.fastq.gz
locustag: "PNUSAC001372"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001373:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001373_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001373_2.fastq.gz
locustag: "PNUSAC001373"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001374:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001374_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001374_2.fastq.gz
locustag: "PNUSAC001374"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001375:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001375_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001375_2.fastq.gz
locustag: "PNUSAC001375"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001376:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001376_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001376_2.fastq.gz
locustag: "PNUSAC001376"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001377:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001377_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001377_2.fastq.gz
locustag: "PNUSAC001377"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001378:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001378_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001378_2.fastq.gz
locustag: "PNUSAC001378"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001379:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001379_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001379_2.fastq.gz
locustag: "PNUSAC001379"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001380:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001380_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001380_2.fastq.gz
locustag: "PNUSAC001380"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001381:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001381_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001381_2.fastq.gz
locustag: "PNUSAC001381"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001382:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001382_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001382_2.fastq.gz
locustag: "PNUSAC001382"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001383:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001383_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001383_2.fastq.gz
locustag: "PNUSAC001383"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
PNUSAC001552:
fw: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001552_1.fastq.gz
rv: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/PNUSAC001552_2.fastq.gz
locustag: "PNUSAC001552"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
genomes:
Campylobacter-jejuni-subsp-jejuni-110-21:
fasta: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/Campylobacter-jejuni-subsp-jejuni-110-21.fasta
locustag: "Campylobacter-jejuni-subsp-jejuni-110-21"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
Campylobacter-jejuni-subsp-jejuni-atcc-33560:
fasta: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/Campylobacter-jejuni-subsp-jejuni-atcc-33560.fasta
locustag: "Campylobacter-jejuni-subsp-jejuni-atcc-33560"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
Campylobacter-jejuni-subsp-jejuni-NCTC11168:
fasta: /home/mostafa.abdel/aProjects/Campylobacter/typingAccreditation/outbreaks/Oakeson-2018/dataset/Campylobacter-jejuni-subsp-jejuni-NCTC11168.fasta
locustag: "Campylobacter-jejuni-subsp-jejuni-NCTC11168"
genustag: "Campylobacter"
taxonomy: "Campylobacter"
DB:
minikraken: /home/mostafa.abdel/dbs/miniKraken/minikraken_20171019_8GB
kraken: /home/DB_RAM/KrakenDB
krona: /home/DB/Krona_Taxonomy
AMR_db: /data/AGr110/mostafa/ariba_fmt_dbs/ariba_Card
VF_db: /data/AGr110/mostafa/ariba_fmt_dbs/ariba_vfdb_full
micDATA: /home/mostafa.abdel/aProjects/Campylobacter/snakemakeProject/Final-Snake-Project/data/micData.txt
AMR_db_abricate: card
VF_db_abricate: vfdb
tools:
scripts_dir: /home/mostafa.abdel/aProjects/Campylobacter/snakemakeProject/Final-Snake-Project/Scripts
multiqc_bin: /home/mostafa.abdel/.local/bin
directories:
snakemake_folder: /home/mostafa.abdel/aProjects/Campylobacter/snakemakeProject/Final-Snake-Project