Ecoli germany: Difference between revisions

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


== Assembly stats ==
== 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
 
* Method:
  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
  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 assembly stats run1-5 ==
   .                        elem      min    q1    q2    q3    max        mean      n50        sum             
   .                        elem      min    q1    q2    q3    max        mean      n50        sum             
   CA.ctg+deg                22395      64    107    159    253    2367      204        216        4567575         
   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
   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
   AMOScmp.Ecoli_55989.ctg  1321      65    425    1780  5257  40345      3774      7775      4985978

Revision as of 13:45, 5 June 2011

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

Links

Assemblies

EdgeBio CLC & newbler

 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 
  • Method:
 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
 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 assembly stats 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