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