Clostridium botulinum
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Data sources
Sanger:
Hall strain A (ATCC 3502) chromosome: 3,886,916 bp 28.24 GC% plasmid: 16,344 bp 26.80 GC% genes: 3,616
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
17K reads missing from Sanger ftp
78,975 Sanger reads
Cbot[1-9]*.[pq][12] 68028 #article: insert sizes of 1.5–2.kb and 2.0–2.kb, 2.2–2.kb, and 2.5–4.0 kb CbBAC1*.s1c 305 CbBAC4*.[pq]1c 430 CbBAC7*.[spq]1c 474 Cbot_ends*.[pq]1c 1604 #article: 19 kb inserts (2kb stdev) ; based on nucmer alignements: 9kb inserts (2kb stdev) CBOT[1-9]*.[pqw] 509 #415 primer walks CBOTC 166 #all primer walks J*.[pqs] 7459 Total 78976
77250 reads aligned by nucmer -c 30 to the reference reads were trimmed based on alignment avgReadLen=503 avgReadClr=499
NCBI:
Name Length %GC AM412317.1 3886916 28.24 # chromosome AM412318.1 16344 26.80 # plasmid pBOT3502 3574 chromosome genes 114 chromosome rRNA's 18 plasmid genes
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;
- 1,604 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.
- 9,343 directed sequencing reads were generated during finishing.
(Total 80,579 reads => 17,464 missing from ftp site)
Assembly
Location:
/fs/szasmg/Bacteria/C_botulinum /fs/szdata/ncbi/genomes/Bacteria/Clostridium_botulinum_A/
2007_0725_WGA
on the 63,115 Sanger reads runCA-OBT.pl (default params) location: 2007_0725_WGA => 109 scaffolds, 243 contigs, 3,823,075 bp => library inser estimates mean=1840.917 stdev=866.039
2007_0801_AMOScmp-relaxed
on the 63,115 Sanger reads MINCLUSTER=30 , MAXTRIM=50 => 2 scaffolds, 148 contigs, 3,883,789 bp CB.qc CB.chromo.png CB.plasmid.png CB-scaff.png
2007_0830_WGA
on the 78,975 Sanger reads; no OBT => 81 scaff, 106 contigs, 3,873,432 bp
2007_0830_AMOScmp-relaxed
on the 78,975 Sanger reads => 2 scaff, 24 contigs, 3,902,812 bp
2007_0831_AMOScmp-relaxed
on the 78,975 Sanger reads => 2 scaff, 22 contigs, 3,902,971 bp
2007_0904_AMOScmp-nucmer -> best
on the 78,975 Sanger reads reads have been trimmed to their maximum alignment coordinates => 2 scaff, 2 contigs, 3,903,275 bp 1 3886795 28.25 (121 bp shorter than the reference) 2 16344 26.80 Gene mappings: /fs/szasmg/Bacteria/C_botulinum/2007_0904_AMOScmp-nucmer/nucmer-genes/CB.ptt