Difference between revisions of "Francisella tularensis"
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| Line 31: | Line 31: | ||
Final assembly steps: | Final assembly steps: | ||
| − | 1. Reads were downloaded from TA and formatted using tarchive2ca | + | 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 | BFTBP: #reads=58051 , insert_mean=2000, insert_stdev=666 | ||
BFTDP: #reads=10409 , 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 | BFTBP: insert_mean=2690.042, insert_stdev=643.126 | ||
BFTDP: insert_mean=3675.914, insert_stdev=1225 | 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 | 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 | |
| − | flanking the problem regions | + | 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: | Final assembly location: | ||
Revision as of 19:49, 8 August 2007
Data sources:
NCBI:
Broad:
Baylor:
Type A:
FSC033 : Broad assembly (15 contigs)
Assemblies location:
/fs/szasmg/Bacteria/F_tularensis_tularensis_FSC033/
Type B:
OSU18 : BCM 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:
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best
Assembly locations:
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/