Francisella tularensis holarctica 275 - Revision history

Dpuiu at 21:25, 15 January 2008

2008-01-15T21:25:52Z

← Older revision		Revision as of 21:25, 15 January 2008
Line 1:		Line 1:
			OLD PAGE: Error : Should be "Francisella tularensis holarctica 257" instead of "Francisella tularensis holarctica 275"

	Center: Broad		Center: Broad
	Status: Assembly (31 contigs)		Status: Assembly (31 contigs)

Dpuiu: /* Assembly */

2007-08-23T15:32:08Z

Assembly

← Older revision		Revision as of 15:32, 23 August 2007
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	Center: Broad		Center: Broad
	Status: Assembly (31 contigs)		Status: Assembly (31 contigs)

Line 60:		Line 60:
	/fs/szasmg2/Bacteria/F_tularensis_tularensis_257		/fs/szasmg2/Bacteria/F_tularensis_tularensis_257

	'''2007_0822_WGA'''		'''2007_0822_WGA -> best'''

	Only WGS reads		Only WGS reads

Dpuiu at 13:45, 23 August 2007

2007-08-23T13:45:55Z

← Older revision		Revision as of 13:45, 23 August 2007
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	Center: Broad		Center: Broad
	Status: Assembly (31 contigs)		Status: Assembly (31 contigs)

Line 71:		Line 71:
	OBT 27116 64 638 971 16274337 600.17 171.69 683		OBT 27116 64 638 971 16274337 600.17 171.69 683

	lib: G878A1 mean=4217 stdev=123 (smaller than original ~~value~~)		lib: G878A1 mean=4217 stdev=123 (smaller than original values)
	=> 10 scaff, 33 contigs, 1,861,251 bp		=> 10 scaff, 33 contigs, 1,861,251 bp

	'''2007_0822_AMOScmp-OBT-454'''		'''2007_0822_AMOScmp-OBT-454'''
	=> 26 scaff, 45 contigs, 1,848,389 bp		=> 26 scaff, 45 contigs, 1,848,389 bp

Dpuiu: /* Assembly */

2007-08-22T19:28:56Z

Assembly

← Older revision		Revision as of 19:28, 22 August 2007
Line 74:		Line 74:
	=> 10 scaff, 33 contigs, 1,861,251 bp		=> 10 scaff, 33 contigs, 1,861,251 bp

	'''2007_0822_AMOScmp-OBT'''		'''2007_0822_AMOScmp-OBT-454'''
	=> 26 scaff, 45 contigs, 1,848,389 bp		=> 26 scaff, 45 contigs, 1,848,389 bp

Dpuiu: /* Assembly */

2007-08-22T19:22:20Z

Assembly

← Older revision		Revision as of 19:22, 22 August 2007
Line 1:		Line 1:
	Center: Broad		Center: Broad
	Status: Assembly (31 contigs)		Status: Assembly (31 contigs)

Line 75:		Line 75:

	'''2007_0822_AMOScmp-OBT'''		'''2007_0822_AMOScmp-OBT'''
			=> 26 scaff, 45 contigs, 1,848,389 bp

Dpuiu at 18:19, 22 August 2007

2007-08-22T18:19:01Z

← Older revision		Revision as of 18:19, 22 August 2007
Line 73:		Line 73:
	lib: G878A1 mean=4217 stdev=123 (smaller than original value)		lib: G878A1 mean=4217 stdev=123 (smaller than original value)
	=> 10 scaff, 33 contigs, 1,861,251 bp		=> 10 scaff, 33 contigs, 1,861,251 bp

			'''2007_0822_AMOScmp-OBT'''

Dpuiu at 18:00, 22 August 2007

2007-08-22T18:00:10Z

← Older revision		Revision as of 18:00, 22 August 2007
Line 1:		Line 1:
	Center: Broad		Center: Broad
	Status: Assembly (31 contigs)		Status: Assembly (31 contigs)

Dpuiu: /* Assembly */

2007-08-22T17:59:13Z

Assembly

← Older revision		Revision as of 17:59, 22 August 2007
Line 1:		Line 1:
	Center: Broad		Center: Broad
	Status: Assembly (31 contigs)		Status: Assembly (31 contigs)

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	== Assembly ==		== Assembly ==

			'''Location'''
			/fs/szasmg2/Bacteria/F_tularensis_tularensis_257

	'''2007_0822_WGA'''		'''2007_0822_WGA'''

Dpuiu at 17:57, 22 August 2007

2007-08-22T17:57:56Z

New page

Center: Broad
Status: Assembly (31 contigs)

== Data ==

'''Reference'''

Name Length %GC
NZ_AAUD01000001.1 36812 31.84
NZ_AAUD01000002.1 115617 32.08
NZ_AAUD01000003.1 102890 32.92
NZ_AAUD01000004.1 10327 35.19
NZ_AAUD01000005.1 51099 32.65
NZ_AAUD01000006.1 20543 32.96
NZ_AAUD01000007.1 27261 32.36
NZ_AAUD01000008.1 31779 33.38
NZ_AAUD01000009.1 35088 32.87
NZ_AAUD01000010.1 6394 32.48
NZ_AAUD01000011.1 71129 32.23
NZ_AAUD01000012.1 33752 32.51
NZ_AAUD01000013.1 12799 30.66
NZ_AAUD01000014.1 69654 32.39
NZ_AAUD01000015.1 270437 31.82
NZ_AAUD01000016.1 3155 35.06
NZ_AAUD01000017.1 3610 30.28
NZ_AAUD01000018.1 3425 32.26
NZ_AAUD01000019.1 3601 34.35
NZ_AAUD01000020.1 6135 29.85
NZ_AAUD01000021.1 7998 32.42
NZ_AAUD01000022.1 6110 33.16
NZ_AAUD01000023.1 3321 31.95
NZ_AAUD01000024.1 245186 31.03
NZ_AAUD01000025.1 141312 30.64
NZ_AAUD01000026.1 103447 31.73
NZ_AAUD01000027.1 242782 32.10
NZ_AAUD01000028.1 67966 32.93
NZ_AAUD01000029.1 57895 33.98
NZ_AAUD01000030.1 77546 34.12
NZ_AAUD01000031.1 17171 32.39
Total 1886241

'''Libraries:'''

CENTER PROJECT STRAIN LIB TYPE SIZE STDEV COUNT LOCATION
WIBR G878 275 G878A1 WGS 4,500 450 23,808 TA
WIBR G878 275 G878A2 WGS 4,500 450 768 TA
WIBR G878 275 G878A3 WGS 4,500 450 768 TA
WIBR G878 275 G878A4 WGS 4,500 450 768 TA
WIBR G878 275 G878A5 WGS 4,500 450 768 TA
WIBR G878 275 G878A9 WGS 10,000 1,000 768 TA
WIBR G878 275 G878A10 WGS 10,000 1,000 768 TA
WIBR G878 275 G878A11 WGS 10,000 1,000 768 TA
WIBR G878 275 G878A12 WGS 10,000 1,000 768 TA
WIBR R95... 257 454-255 454 . . 901,724 TA
Total 931,676

== Assembly ==

'''2007_0822_WGA'''

Only WGS reads
runCA-OBT.pl => new read clr, new library insert estimates

clr got shorter by runing OBT (usually is the opposite)

. #traces min median max sum mean stdev n50
CLIPPING 29397 0 908 1116 25713268 874.69 137.9 916
OBT 27116 64 638 971 16274337 600.17 171.69 683

lib: G878A1 mean=4217 stdev=123 (smaller than original value)
=> 10 scaff, 33 contigs, 1,861,251 bp