Difference between revisions of "Clostridium botulinum"

From Cbcb
Jump to navigation Jump to search
Line 48: Line 48:
   [https://wiki.umiacs.umd.edu/cbcb/images/b/b8/CB.2007_0801_AMOScmp-relaxed.chromo.png CB.chromo.png]
   [https://wiki.umiacs.umd.edu/cbcb/images/b/b8/CB.2007_0801_AMOScmp-relaxed.chromo.png CB.chromo.png]
   [https://wiki.umiacs.umd.edu/cbcb/images/9/97/CB.2007_0801_AMOScmp-relaxed.plasmid.png CB.plasmid.png]
   [https://wiki.umiacs.umd.edu/cbcb/images/9/97/CB.2007_0801_AMOScmp-relaxed.plasmid.png CB.plasmid.png]
  [https://wiki.umiacs.umd.edu/cbcb/images/a/a2/CB-scaff.2007_0801_AMOScmp-relaxed.png CB-scaff.png]

Revision as of 14:51, 9 August 2007

Data sources


 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
   there are 124 regions in the reference which are not covered by reads


 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. A further 9343 directed sequencing reads were generated during finishing.



  • 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
  • AMOScmp
  location: 2007_0801_AMOScmp-relaxed
  => 2 scaffolds, 148 contigs