Clostridium botulinum: Difference between revisions
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CLR=1,len(read) | CLR=1,len(read) | ||
there are 124 regions in the reference which are not covered by reads | there are 124 regions in the reference which are not covered by reads | ||
NCBI : | |||
Reads have not been submitted to TA | |||
* [http://www.genome.org/cgi/reprint/gr.6282807v1 Paper] | |||
== Assembly == | == Assembly == | ||
Location: | |||
/fs/szasmg/Bacteria/C_botulinum | /fs/szasmg/Bacteria/C_botulinum | ||
| Line 32: | Line 37: | ||
=> 109 scaffolds, 243 contigs | => 109 scaffolds, 243 contigs | ||
=> library inser estimates mean=1840.917 stdev=866.039 | => library inser estimates mean=1840.917 stdev=866.039 | ||
Revision as of 14:05, 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
NCBI :
Reads have not been submitted to TA
Assembly
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