Ecoli germany

Finished genomes

 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
 ...

 NC_004914      Stx2 converting phage II, complete genome                             Length: 62,706 nt

Data

• BGI Sequences Genome of the Deadly E. Coli in Germany and Reveals New Super-Toxic Strain June 2nd 2011
• BGI run1-7 & assembly

 .         elem         min  q1   q2   q3    max    mean  n50    sum
 run1      92370        5    99   106  109   123    102   107    9433083
 run2      122208       5    96   105  109   133    100   106    12248530
 run3      96765        5    100  106  110   129    103   107    9958873
 run4      222275       5    101  107  110   135    103   107    22924825
 run5      95750        5    92   103  108   133    97    104    9379125
 run1-5    629368       5    99   106  109   135    102   107    63944436  (12.2X)
 
 run6      79341        5    104  108  111   137    105   108    8355410
 run7      74388        5    97   105  109   129    100   106    7469876
 run1-7    783097       5    99   106  110   137    102   107    79769722  (15.2X)
 
 ctg       1217         100  251  938  5215  72019  4274  13577  5201850
 ctg.v2    513          62   346  896  4903  204342 10330 53266  5299150

• Escherichia coli TY-2482, whole genome shotgun sequencing project @NCBI

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/
• [1]

EdgeBio Assembly

• Used 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.

CBCB best assembly

• run1-5

 .             elem  min  q1   q2   q3    max     mean   n50    sum     
 ctg           505   35   204  758  8927  185186  9823   41503  4960767 
 ctg.denovo    4261  31   41   58   104   2713    119    31     506842  
 total         4766  31   44   59   161   185186  1147   41503  5467609 

• run1-7

 .             elem  min  q1   q2   q3    max     mean   n50    sum            
 ctg           445   41   202  651  7622  185186  11156  46725  4964630        
 ctg.denovo    4704  31   39   57   88    2990    113    31     531947         
 total         5149  31   40   58   129   185186  1068   46725  5496577        

• Method (run1-5):

 The reads were first assembled using Ecoli_55989 as reference. The unmapped reads were assembled denovo using ABYSS. 
 total reads: 629,368
 reads aligned to Ecoli_55989 using "bwa bwasw": 545,233 (the consensus was called using "samtools pileup")
 unaligned reads : 84,135

• Ftp file locations (run1-5)

 ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/
 ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/assemble.sh
 ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/asm.summary
 ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/asm.ctg.fasta
 ftp://ftp.cbcb.umd.edu/pub/data/assembly/Ecoli_TY-2482/asm.ctg.denovo.fasta

Other CBCB assemblies run1-5

 .                         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