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 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) | ||
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* [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: | |||
* 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