Francisella tularensis holarctica OSU18

Center: Baylor Status: Complete

Data

Reference:

 NC_008369.1

Libraries:

 CENTER        PROJECT	        STRAIN	SEQ_LIB_ID	        TYPE	SIZE	STDEV	COUNT	Location	Comment
 BCM  	        BFTB	        OSU-18	BFTBP	                WGS	2,000	1,000	58,053	TA	        acc=3379596; INSERT_SIZE,STD=2690,643 (WGA)
 BCM	        BFTD	        OSU-18	BFTDP	                WGS	2,000	1,000	10,409	TA	        acc=3379603; INSERT_SIZE,STD=3675,1407 (WGA)
 BCM	        4WG_FTOS	OSU18	4WGS_FTOSA	        454	.	.	310,747	TA	
 BCM	        4WG_FTUL.OS	OSU18	4WG_FTUL.OS_000pA	454	.	.	216,495	SRA	        ?
 StrainSubtotal                                                                        595,704		        Baylor site: 65,131 Sanger & 317,789 454 Reads

Assembly

Location:

 /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/

Steps:

 1. The complete genome sequence was downloaded from NCBI: NC_008369.1
 2. Reads were downloaded from TA and formatted using tarchive2ca 
 3. Only the 2 Sanger libraries for this project were considered
      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