Difference between revisions of "Francisella tularensis"

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OSU18 : BCM complete
 
OSU18 : BCM complete
  
Assembly steps:
+
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 reads
+
       BFTBP: #reads=58051 , insert_mean=2000, insert_stdev=666
       BFTDP:10409 reads
+
       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 
  
Assemblies location:
 
  /fs/szasmg/Bacteria/F_tularensis_holarctica_OSU18/
 
  
 
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/

Novicida

Mediasiatica