Difference between revisions of "Francisella tularensis"

From Cbcb
Jump to navigation Jump to search
Line 28: Line 28:
 
== Type B: ==
 
== Type B: ==
  
OSU18 : BCM complete
+
[https://wiki.umiacs.umd.edu/cbcb/index.php/Francisella_tularensis_holarctica_OSU18 OSU18] Baylor, Complete
 
 
Assembly locations:
 
  /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/
 
 
 
Final assembly steps:
 
  1. The complete genome sequence was downloaded from NCBI: NC_008369.1
 
  2. Reads were downloaded from TA and formatted using tarchive2ca
 
  3. There are 2 Sanger libraries for this project
 
      BFTBP: #reads=58051 , insert_mean=2000, insert_stdev=666
 
      BFTDP: #reads=10409 , insert_mean=2000, insert_stdev=666
 
  4. The reads have been retrimmed using veraTrim (-T 10 -M 100 -E 500)
 
  5. runCA-OBT.pl has been used to assemble all the reads
 
    location: 2007_0724_WGA-default/  
 
    =>160 scaff, 163 contigs, 23X coverage
 
  6. The library sizes were updates using the WGA estimates
 
      BFTBP: insert_mean=2690.042, insert_stdev=643.126
 
      BFTDP: insert_mean=3675.914, insert_stdev=1225
 
  7. The WGA was aligned to the reference using nucmer; one rearrangement, one 
 
    deletion and several SNP's were noticed
 
  8. The reads were assembled using AMOScmp (default parameters)
 
    location: 2007_0724_AMOSCMP-default/
 
    => 1 scaffold, 22 contigs
 
    2 missoriented read pile regions were noticed
 
  9. The assembly was aligned to itself; 950 bp inverted repeats were identified as
 
    flanking the problem regions; the coordinates are:
 
      16336-21562  (5  KB)
 
      167086-184936 (17 KB)
 
  10. The 2 regions were flipped ; the new reference is called NC_008369.2
 
  11. Several small contig (step 8) read clear ranges have been extend to their OBT
 
      trimming points
 
  12. AMOScmp was rerun using more relaxed parameters:
 
        nucmer      MINCLUSTER=30
 
        casm-layout MAXTRIM=50
 
    location: 2007_0731_AMOSCMP-veraTrim-updateDst-relaxed-updateClr-fixRef2->best
 
    => 1 scaffold, 8 contigs
 
 
 
Final assembly location:     
 
  /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best
 
  
 
== Novicida ==
 
== Novicida ==
  
 
== Mediasiatica ==
 
== Mediasiatica ==

Revision as of 19:58, 8 August 2007

Data sources:

NCBI:

Broad:

Baylor:

Type A:

FSC033 : Broad assembly (15 contigs)

Assemblies location:

 /fs/szasmg/Bacteria/F_tularensis_tularensis_FSC033/

Type B:

OSU18 Baylor, Complete

Novicida

Mediasiatica