Difference between revisions of "Francisella tularensis holarctica OSU18"
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Revision as of 13:40, 9 August 2007
Center: Baylor Status: Complete
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: