Clostridium botulinum: Difference between revisions
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* [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB.dbs Complete Genome] | * [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB.dbs Complete Genome] | ||
Hall strain A (ATCC 3502) | Hall strain A (ATCC 3502) | ||
chromosome: | chromosome: 3,886,916 bp 28.24 GC% | ||
plasmid: | plasmid: 16,344 bp 26.80 GC% | ||
* [ftp://ftp.sanger.ac.uk/pub/pathogens/cb/CB_shotgun.dbs 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 | NCBI : reads have not been submitted to TA | ||
Revision as of 01:49, 9 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%
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