Clostridium botulinum

Data sources

Sanger:

• Genome Project

• Complete Genome

 Hall strain A (ATCC 3502)
 chromosome: 3,886,916 bp 28.24 GC%
 plasmid:      16,344 bp 26.80 GC%

• 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
     

NCBI : reads have not been submitted to TA