Difference between revisions of "Clostridium botulinum"
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Revision as of 14:51, 9 August 2007
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
Reads have not been submitted to TA
- 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 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.
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
MINCLUSTER=30 , MAXTRIM=50 location: 2007_0801_AMOScmp-relaxed => 2 scaffolds, 148 contigs CB.qc CB.chromo.png CB.plasmid.png CB-scaff.png