View source for 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

  [[Media:NC_008601-NZ_ABAH00000000.png|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