Assembly merge

Cases

No reference assembly

One data set, multiple denovo assemblers

Example:

 * Solexa data
 * edena & velvet assemblers

Solutions:

 * merge 2 assembly sets
 * run minimus on them

Multipls data sets, one(multiple) denovo assemblers

Example:

 Solexa & 454 data
 velvet assemblers for each set

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Examples

Pseudomonas_syringae

Reference:

 Name           Length %GC
 NC_004578.1    6397126 58.40
 NC_004633.1    73661  55.15
 NC_004632.1    67473  56.17

Repeats:

 desc    #elem   min     max     mean    stdev   sum
 50bp+   991     49      7361    392.73  792.41  389201
 100bp+  429     99      7361    814.36  1060.29 349364

Data:

 Type            #reads       min     max     mean
 Solexa          6340136      32      32      32
 Sim(ulated)     6538167      32      32      32
 454             77466        35      371     240

Single assemblies:

 assembler   type         input-data     #reads   #ctgs   min     max     mean            stdev           ctgs-sum        
 
 edena       denovo       Solaxa         6340136  14084   100     5075    210.92          145.68          2970720
 velvet      denovo       Solaxa         6340136  25161   45      5057    241.83          212.61          6084887
 
 edena-sim   denovo       Sim            6538167  2068    100     47881   2994.03         4857.76         6191673
 velvet-sim  denovo       Sim            6538167  2207    45      56810   2820.91         5348.36         6225757
 
 AMOScmp     comparative  Solaxa         6340136  187     20      577929  34863.06        91692.34        6519394      

Merged assemblies:

 assemblers     type         input-data  #reads  #ctgs   min     max     mean            stdev           ctgs-sum        
 edena+velvet   denovo       contigs     39245