Francisella tularensis tularensis FSC033: Difference between revisions

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   lib: G907A3 mean=4274.536 stdev=110.196 (probably underestimate due to low coverage)
   lib: G907A3 mean=4274.536 stdev=110.196 (probably underestimate due to low coverage)
   => 12 scaff, 23 contigs
   => 12 scaff, 23 contigs, 1,882,120 bp


'''2007_0807_AMOScmp-OBT'''
'''2007_0807_AMOScmp-OBT'''
   use  read clr, library insert estimates from 2007_0807_WGA  
   use  read clr, library insert estimates from 2007_0807_WGA  
   => 13 scaff, 23 contigs
   => 13 scaff, 23 contigs, 1,834,339 bp


'''2007_0809_AMOScmp-OBT'''
'''2007_0809_AMOScmp-OBT-454'''
   use  read clr, library insert estimates from 2007_0807_WGA  
   use  read clr, library insert estimates from 2007_0807_WGA  
   include the 454 reads
   include the 454 reads
   => 15 scaff, 20 contigs
   => 15 scaff, 18 contigs, 1,844,162 bp

Revision as of 19:55, 16 August 2007

Center: Broad

 Status: Assembly (15 contigs)

Data

Reference:

 NZ_AAYE00000000
 Name              Length %GC
 NZ_AAYE01000001.1 101124 33.65
 NZ_AAYE01000002.1 46675  32.87
 NZ_AAYE01000003.1 1600   34.25
 NZ_AAYE01000004.1 295522 31.87
 NZ_AAYE01000005.1 650364 31.73
 NZ_AAYE01000006.1 2400   37.29
 NZ_AAYE01000007.1 132212 32.96
 NZ_AAYE01000008.1 23680  31.04
 NZ_AAYE01000009.1 201    45.27      high GC%: 16S-23S rRNA(megablast)
 NZ_AAYE01000010.1 571    46.06      high GC%
 NZ_AAYE01000011.1 61231  32.30
 NZ_AAYE01000012.1 249955 31.91
 NZ_AAYE01000013.1 137017 32.24
 NZ_AAYE01000014.1 91009  32.87
 NZ_AAYE01000015.1 50644  33.42
 Total             1844205          1,892,819 bp in SCHU S4(complete genome)=> ~ 48,614 bp in gaps

Traces: from NCBI TA

Libraries:

 CENTER         PROJECT	STRAIN	LIB	TYPE	SIZE	STDEV	COUNT	Location
 WIBR           G907	033	G907A1	WGS	4,500	450	768	TA
 WIBR	        G907	033	G907A2	WGS	4,500	450	768	TA
 WIBR	        G907	033	G907A3	WGS	4,500	450	20,736	TA
 WIBR	        G907	033	G907A4	WGS	4,500	450	768	TA
 WIBR	        G919	033	454-410	454	.	.	278,235	TA
 StrainSubtotal                                                 301,275
 NC_006570-NZ_AAYE00000000.png Mummerplot  Francisella tularensis subsp. tularensis Schu 4, complete genome vs Francisella tularensis subsp. tularensis FSC033

Assembly

Locations:

 /fs/szasmg/Bacteria/F_tularensis_tularensis_FSC033/

2007_0807_AMOScmp

 Uses default trimming
 AMOScmp
 =>  13 scaff, 32 contigs, 1,830,923 bp

2007_0807_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        22713    1       868     1018    19613029        863.52  68.27   871
 OBT             22207    71      785     907     17128190        771.3   75.98   789
 lib: G907A3 mean=4274.536 stdev=110.196 (probably underestimate due to low coverage)
 => 12 scaff, 23 contigs, 1,882,120 bp 

2007_0807_AMOScmp-OBT

 use  read clr, library insert estimates from 2007_0807_WGA 
 => 13 scaff, 23 contigs, 1,834,339 bp

2007_0809_AMOScmp-OBT-454

 use  read clr, library insert estimates from 2007_0807_WGA 
 include the 454 reads
 => 15 scaff, 18 contigs, 1,844,162 bp