Clostridium botulinum: Difference between revisions

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     no quality      : default 20 assigned to all the bases
     no quality      : default 20 assigned to all the bases
     no mate pairing  : can be inferred from names (.p1c, .q1c => 27,331 mates); however there seem to be many errors (links from chromosome to the plasmid)
     no mate pairing  : can be inferred from names (.p1c, .q1c => 27,331 mates); however there seem to be many errors (links from chromosome to the plasmid)
    no library info  : assumed there was only one library used
''    no library info  : assumed there was only one library used
     no trimming info : almost all reads have "CONTAINED" alignments to the reference
     no trimming info : almost all reads have "CONTAINED" alignments to the reference
                       CLR=1,len(read)
                       CLR=1,len(read)
Line 28: Line 28:
* [http://www.genome.org/cgi/reprint/gr.6282807v1 Paper: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes; Genome Res. published online May 22, 2007]
* [http://www.genome.org/cgi/reprint/gr.6282807v1 Paper: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes; Genome Res. published online May 22, 2007]


''The initial genome assembly was obtained from:
The initial genome assembly was obtained from:
* 69,632 paired end sequences (giving 9.15-fold coverage) derived from four genomic shotgun libraries (all in pUC18 with insert sizes of 1.5–2.0 kb and 2.0–2.2 kb, 2.2–2.5 kb, and 2.5–4.0 kb) using dye terminator chemistry on ABI3700 automated sequencers;  
* 69,632 paired end sequences (giving 9.15-fold coverage) derived from four genomic shotgun libraries (all in pUC18 with insert sizes of 1.5–2.0 kb and 2.0–2.2 kb, 2.2–2.5 kb, and 2.5–4.0 kb) using dye terminator chemistry on ABI3700 automated sequencers;  
* 1604 pairedend sequences from one pBACe3.6 library with insert sizes of 15–23 kb (a clone coverage of 3.9-fold) were used as a scaffold.  
* 1604 pairedend sequences from one pBACe3.6 library with insert sizes of 15–23 kb (a clone coverage of 3.9-fold) were used as a scaffold.  
* 9343 directed sequencing reads were generated during finishing.
* 9343 directed sequencing reads were generated during finishing.
''


== Assembly  ==
== Assembly  ==

Revision as of 15:52, 20 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%
 Mummerplot: Complete Genome vs Complete Genome
 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); however there seem to be many errors (links from chromosome to the plasmid)

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

NCBI :

 Reads have not been submitted to TA

The initial genome assembly was obtained from:

  • 69,632 paired end sequences (giving 9.15-fold coverage) derived from four genomic shotgun libraries (all in pUC18 with insert sizes of 1.5–2.0 kb and 2.0–2.2 kb, 2.2–2.5 kb, and 2.5–4.0 kb) using dye terminator chemistry on ABI3700 automated sequencers;
  • 1604 pairedend sequences from one pBACe3.6 library with insert sizes of 15–23 kb (a clone coverage of 3.9-fold) were used as a scaffold.
  • 9343 directed sequencing reads were generated during finishing.

Assembly

2007_0725_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

2007_0801_AMOScmp-relaxed

  MINCLUSTER=30 , MAXTRIM=50
  => 2 scaffolds, 148 contigs
 CB.qc
 CB.chromo.png
 CB.plasmid.png
 CB-scaff.png

Location:

 /fs/szasmg/Bacteria/C_botulinum