Francisella tularensis: Difference between revisions
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| Line 30: | Line 30: | ||
OSU18 : BCM complete | OSU18 : BCM complete | ||
Final assembly steps: | |||
1. Reads were downloaded from TA and formatted using tarchive2ca | 1. Reads were downloaded from TA and formatted using tarchive2ca | ||
2. There are 2 Sanger libraries for this project | 2. There are 2 Sanger libraries for this project | ||
BFTBP:58051 | BFTBP: #reads=58051 , insert_mean=2000, insert_stdev=666 | ||
BFTDP:10409 | BFTDP: #reads=10409 , insert_mean=2000, insert_stdev=666 | ||
3. The reads have been retrimmed using veraTrim (-T 10 -M 100 -E 500) | 3. The reads have been retrimmed using veraTrim (-T 10 -M 100 -E 500) | ||
4. runCA-OBT.pl has been used to assemble all the reads | 4. runCA-OBT.pl has been used to assemble all the reads | ||
5. The library sizes were updates using the WGA estimates | 5. 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 | |||
6. The WGA was aligned to the reference using nucmer; one rearrangement, one | 6. 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 | ||
7. The reads were assembled using AMOScmp (default parameters); 2 missoriented | |||
read pile regions were noticed | |||
8. The assembly was aligned to itself; 950 bp inverted repeats were identified as | |||
flanking the problem regions | |||
9. The 2 regions were flipped | |||
Final assembly location: | Final assembly location: | ||
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best | /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best | ||
Assembly locations: | |||
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/ | |||
== Novicida == | == Novicida == | ||
== Mediasiatica == | == Mediasiatica == | ||
Revision as of 19:36, 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. Reads were downloaded from TA and formatted using tarchive2ca
2. 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
3. The reads have been retrimmed using veraTrim (-T 10 -M 100 -E 500)
4. runCA-OBT.pl has been used to assemble all the reads
5. 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
6. The WGA was aligned to the reference using nucmer; one rearrangement, one
deletion and several SNP's were noticed
7. The reads were assembled using AMOScmp (default parameters); 2 missoriented
read pile regions were noticed
8. The assembly was aligned to itself; 950 bp inverted repeats were identified as
flanking the problem regions
9. The 2 regions were flipped
Final assembly location:
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best
Assembly locations:
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/