Francisella tularensis novicida GA99-3548

 Center: Broad
 Status: Assembly (18 contigs)

Data

Reference:

 Name           Length %GC
 NZ_ABAH01000001.1 77907  33.26
 NZ_ABAH01000002.1 3200   35.62
 NZ_ABAH01000003.1 143439 32.80
 NZ_ABAH01000004.1 4000   35.33
 NZ_ABAH01000005.1 55000  33.33
 NZ_ABAH01000006.1 336    46.73  high GC%
 NZ_ABAH01000007.1 560    34.29
 NZ_ABAH01000008.1 623050 31.76
 NZ_ABAH01000009.1 18017  32.28
 NZ_ABAH01000010.1 238333 32.07
 NZ_ABAH01000011.1 312    44.23  high GC%
 NZ_ABAH01000012.1 466    44.21  high GC%
 NZ_ABAH01000013.1 293238 32.05
 NZ_ABAH01000014.1 171625 34.06
 NZ_ABAH01000015.1 1155   48.14  high GC%
 NZ_ABAH01000016.1 344    46.80  high GC%
 NZ_ABAH01000017.1 301    46.18  high GC%
 NZ_ABAH01000018.1 214208 32.15
 Total             1,845,491 bp     1,910,031 bp in U112(complete) => 64,540 bp in gaps

Traces: from NCBI TA

Libraries:

 CENTER  PROJECT   STRAIN     LIB     TYPE   SIZE STDEV   COUNT   Location
 WIBR    G909      GA99-3548  G909A2  WGS    4,500 450    768     TA
 WIBR    G909      GA99-3548  G909A4  WGS    4,500 450    768     TA
 WIBR    G909      GA99-3548  G909A3  WGS    4,500 450    23,040  TA
 WIBR    G921      GA99-3548  454-414 454    .     .      17,731  TA
 Total                                                    42,307

 NC_008601-NZ_ABAH00000000.png 
 Mummerplot  Francisella tularensis noviciada U112 (complete genome) vs Francisella tularensis novicida GA99-3548
 No rearrangements can be noticed; several indels (up to 24KB)

Assembly

Locations

 /fs/szasmg2/Bacteria/F_tularensis_novicida_GA99-3548

2007_0816_AMOScmp

 Uses default trimming
  =>  11 scaff, 24 contigs, 1,830,675 bp

2007_0816_WGA -> best

 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        23721    0       857     1034    20118102        848.11  77.58   859
 OBT             22543    65      783     917     17315299        768.1   76.93   786

 lib: G909A3 mean=5996.958 stdev=144.620 (larger insert than original value)
 => 8 scaff, 18 contigs, 1,839,522 bp

2007_0816_AMOScmp-OBT

use  read clr from 2007_0807_WGA 
=> 13 scaff, 23 contigs, 1,832,735 bp
autoJoiner was run on this assembly ; reference ID's had to be "truncated" ([^|.]); no gaps were filled

2007_0820_AMOScmp-OBT-454

use  read clr from 2007_0807_WGA  + 454 reads
=> 13 scaff, 35 contigs,  1,839,125 bp