Ecoli germany

Close relatives

   NC_011748	   Escherichia coli 55989, complete genome;                              Length: 5,154,862 nt
   NC_011752	   Escherichia coli 55989 plasmid 55989p, complete sequence;             Length: 72,482 nt

   NC_013353	   Escherichia coli O103:H2 str. 12009, complete genome;                 Length: 5,449,314 nt
   NC_013354	   Escherichia coli O103:H2 str. 12009 plasmid pO103, complete sequence; Length: 75,546 nt

Data

• http://www.genomics.cn/en/news_show.php?type=show&id=644
• ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/

Links

• http://www.iontorrent.com/
• http://omicsomics.blogspot.com/2011/05/ion-torrents-data-quality-is-pretty.html
• http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/

Assemblies

EdgeBio CLC & newbler

• http://www.edgebio.com/data/ion/ecoli_bgi/

 read QC: FastQC 
 read trimming: CLC

 .                    elem       min    q1     q2     q3     max        mean       n50        sum          
 run                  629368     5      99     106    109    135        102        107        63944436 
 run.trimmed          617257     10     46     69     86     94         64         79         39745910   

 read alignment: CLC; 85% of untrimmed reads aligned
 6X+ cvg regions: 490 SNPS s & 1,848 INDELS.  

 De novo assembly of 90K reads that did not map, 58K assembled together => 363 contigs ranging in size from 400 to 7800 bp.  
 Contigs were blasted against NRNT at NCBI with a minimum .01 e-value. 
 Hits:  E. coli strains (such as O83:H1 and O42) , Shigella flexneri, Salmonella, and Cronobacter.  

 De novo assembly => 3,297 contigs with an N25 of 4K and N50 of 2.5K.

Assembly stats

 .                         elem       min    q1     q2     q3     max        mean       n50        sum            
 CA.ctg+deg                22395      64     107    159    253    2367       204        216        4567575        
 newbler.Ecoli_55989.ctg   8357       100    218    397    696    5038       534        639        4465330
 AMOScmp.Ecoli_55989.ctg   1321       65     425    1780   5257   40345      3774       7775       4985978