Difference between revisions of "Clostridium botulinum"

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Line 7: Line 7:
 
* [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB.dbs Complete Genome]
 
* [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB.dbs Complete Genome]
 
   Hall strain A (ATCC 3502)
 
   Hall strain A (ATCC 3502)
   chromosome: 3886916 bp 28.24 GC%
+
   chromosome: 3,886,916 bp 28.24 GC%
   plasmid:      16344 bp 26.80 GC%
+
   plasmid:      16,344 bp 26.80 GC%
 +
 
 +
* [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB_shotgun.dbs Traces]
 +
  63,115 Sanger reads
 +
 
 +
  Read problems:
 +
    no quality      : default 20 assigned to all the bases
 +
    no mate pairing  : can be inferred from names (.p1c, .q1c => 27,331 mates)
 +
    no library info  : assumed there was only one library used
 +
    no trimming info : almost all reads have "CONTAINED" alignments to the reference
 +
                      CLR=1,len(read)
 +
    there are 124 regions in the reference which are not covered by reads
 +
 
 +
== Assembly  ==
 +
 
 +
Assemby location:
 +
  /fs/szasmg/Bacteria/C_botulinum
 +
 
 +
* WGA
 +
    create a .frg file
 +
    runCA-OBT.pl (default params)
 +
    location: 2007_0725_WGA/
 +
    => 109 scaffolds, 243 contigs
 +
 
 +
 
 +
    => library inser estimates mean=1840.917 stdev=866.039
 +
     
 +
 
  
* [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB_shotgun.dbs Shorgun Reads]
 
  63115 Sanger reads
 
  no quality      : default 20
 
  no mate pairing  : can be inferred from names (.p1c, .q1c => 27,331 mates)
 
  no trimming info : almost all reads have "CONTAIN
 
  
  
 
NCBI : reads have not been submitted to TA
 
NCBI : reads have not been submitted to TA

Revision as of 01:49, 9 August 2007

Data sources

Sanger:

 Hall strain A (ATCC 3502)
 chromosome: 3,886,916 bp 28.24 GC%
 plasmid:      16,344 bp 26.80 GC%
 63,115 Sanger reads
 Read problems:
   no quality       : default 20 assigned to all the bases
   no mate pairing  : can be inferred from names (.p1c, .q1c => 27,331 mates)
   no library info  : assumed there was only one library used
   no trimming info : almost all reads have "CONTAINED" alignments to the reference
                      CLR=1,len(read)
   there are 124 regions in the reference which are not covered by reads

Assembly

Assemby location:

 /fs/szasmg/Bacteria/C_botulinum
  • WGA
   create a .frg file
   runCA-OBT.pl (default params) 
   location: 2007_0725_WGA/
   => 109 scaffolds, 243 contigs


   => library inser estimates mean=1840.917 stdev=866.039
      
 


NCBI : reads have not been submitted to TA