Difference between revisions of "Francisella tularensis"
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| Line 29: | Line 29: | ||
OSU18 : BCM complete | OSU18 : BCM complete | ||
| + | |||
| + | Assembly steps: | ||
| + | 1. Reads were downloaded from TA and formatted using tarchive2ca | ||
| + | 2. There are 2 Sanger libraries for this project | ||
| + | BFTBP:58051 reads | ||
| + | BFTDP:10409 reads | ||
| + | 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 | ||
| + | 6. The WGA was aligned to the reference using nucmer; one rearrangement, one deletion and several SNP's were noticed | ||
Assemblies location: | Assemblies location: | ||
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/ | /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/ | ||
| − | Final assembly: | + | Final assembly location: |
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best | /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best | ||
Revision as of 19:28, 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
Assembly steps:
1. Reads were downloaded from TA and formatted using tarchive2ca
2. There are 2 Sanger libraries for this project
BFTBP:58051 reads
BFTDP:10409 reads
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
6. The WGA was aligned to the reference using nucmer; one rearrangement, one deletion and several SNP's were noticed
Assemblies location:
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/
Final assembly location:
/fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/best