Francisella tularensis holarctica OSU18
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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