View source for F tularensis holarctica OSU18

Center: Baylor
Status: 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