Difference between revisions of "Clostridium botulinum"

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Line 31: Line 31:
 
     location: 2007_0725_WGA/
 
     location: 2007_0725_WGA/
 
     => 109 scaffolds, 243 contigs
 
     => 109 scaffolds, 243 contigs
 
 
 
     => library inser estimates mean=1840.917 stdev=866.039
 
     => library inser estimates mean=1840.917 stdev=866.039
     
+
     
 
 
 
 
  
  
 
NCBI : reads have not been submitted to TA
 
NCBI : reads have not been submitted to TA

Revision as of 03:38, 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