Assembly merge: Difference between revisions

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Assemblies:
Assemblies:
   Assembler      type         input-data  #reads         #ctgs  min    max    mean      stdev      ctgs-sum      #singletons    comments
   Assembler      type        #ctgs  min    max    mean      stdev      ctgs-sum      #singletons    comments
   AMOSCmp-PA14  comparative  Solexa      8627900        2053    17      170485  3011.84  11917.53  6183320      1127399
   AMOSCmp-PA14  comparative  2053    17      170485  3011.84  11917.53  6183320      1127399
   AMOSCmp-PAO1  comparative  Solexa      8627900        2797    17      75626  2161.19  5812.2    6044851      1592525
   AMOSCmp-PAO1  comparative  2797    17      75626  2161.19  5812.2    6044851      1592525
   AMOScmp-PA2192 comparative  Solexa      8627900        5816    17      133129  1072.8    3725.22    6239454      1601299        largest assembly
   AMOScmp-PA2192 comparative  5816    17      133129  1072.8    3725.22    6239454      1601299        largest assembly
   velvet        denovo      Solexa      8627900        10684  45      16239  640.34    825.24    6841458      ?              much better than Ps !!!
   velvet        denovo      10684  45      16239  640.34    825.24    6841458      ?              much better than Ps !!!
   edena          denovo      Solexa      8627900        11180  100    11300  552.36    610.52    6175460      3955865 (46%)  much better than Ps !!!
   edena          denovo      11180  100    11300  552.36    610.52    6175460      3955865 (46%)  much better than Ps !!!
  sake          denovo      185030  34      5490    77.21  141.23  14287079


Merged assemblies(contigs&singletons):
Merged assemblies(contigs&singletons):
   Assembler          type  input-data          #reads  #ctgs  min  max    mean    stdev      ctgs-sum      comments
   Assembler          type  input-data          #reads  #ctgs  min  max    mean    stdev      ctgs-sum      comments
   AMOSCmp-PA14-merge  ?      AMOSCmp-PA14(ctgs)  2053    1931    17    170485  3201.7  12981.57  6182486        2053-1931=122 gaps closed
   AMOSCmp-PA14-merge  ?      AMOSCmp-PA14(ctgs)  2053    1931    17    170485  3201.7  12981.57  6182486        2053-1931=122 gaps closed

Revision as of 15:59, 31 March 2008

Assemblers

Denovo

Minimus

* hash-overlap overlap: 
    40 bp default : too large for contig assemblies
    20 bp minimum overlap; minimizer window length must be >=15bp; could these values be dropped lower?
    very slow on large sequences (ex Ps.fasta, Ps.plasmid.fasta) even if USE_SIMPLE_OVERLAP=1 !!! WHY???

Velvet

* overlap:
    18bp usually gives fewest contigs
    24bp is also ok
    15bp is too low => too many short contigs
 
* the coverage levels reported in the contig names look sort of small (by about 3 times smaller than they should be)

Edena

 * contigs don't overlap

Comparative

AMOScmp

Cases

No reference sequence

One data set, multiple denovo assemblers

Example:

 * Solexa data
 * edena & velvet assemblers

Solution:

 * merge 2 assembly contigs
 * run minimus on them

Multipls data sets, one(multiple) denovo assemblers

Example:

 Solexa & 454 data
 velvet assemblers for each set

One reference sequence

Few indels, few rearrangements

Solution:

 * AMOScmp
 * If there are many negative gaps try to further join contigs (fastaMerge.pl $PREFIX.fasta) 

Many indels, few rearrangements

Few indels, many rearrangements

Multiple reference sequences


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    #repeats   min     max     mean    stdev    sum
 50bp+   991        50      7362    393.73  792.41   390192
 100bp+  429        100     7362    815.36  1060.29  349793

Solexa reads

 Type            #reads       min     max     mean
 Solexa          6340136      32      32      32   (~31x coverage)

Assemblies:

 Assembler   type         input-data  #reads         #ctgs   min     max     mean      stdev     ctgs-sum      #singletons       
 AMOScmp     comparative  Solaxa      6340136        187     20      577929  34863.06  91692.34  6519394       698638(11%)
 velvet      denovo       Solaxa      6340136        25161   45      5057    241.83    212.61    6084887
 edena       denovo       Solaxa      6340136        14084   100     5075    210.92    145.68    2970720       4893301(77%)

Merged assemblies(contigs&singletons):

 assemblers     type         input-data                #reads  #ctgs   min     max     mean     stdev   ctgs-sum   comments    
 AMOScmp-merged ?            AMOScmp(contigs)          187     166     20      804024  39272.2  121124  6519189    #merged 187-166=21 negative gaps  out of a total of 32
 minimus(ovl20) denovo       velvet(contigs)           25161   19121   45      5057    311.3    297.27  5952381    #merged 25161-19121=6040 (25%) gaps
 minimus(ovl15) denovo       velvet(contigs)           25161   16343   45      9903    361.32   359.78  5905143    #merged 25161-16343=8818 (35%) gaps
 minimus(ovl40) denovo       edena+velvet(contigs)     39245   23644   45      6688    257.15   232.94  6080063    #very few 40bp overlaps are found
 minimus(ovl20) denovo       edena+velvet(contigs)     39245   18603   45      6688    322.32   311.02  5996244

Simulated 32bp exact match reads

 Type            #reads       min     max     mean
 Sim(ulated)     6538167      32      32      32   ( 32x coverage)

Single assemblies:

 Assembler   type         input-data  #reads         #ctgs   min     max     mean      stdev     ctgs-sum      #singletons       
 edena-sim   denovo       Sim         6538167        2068    100     47881   2994.03   4857.76   6191673       198699(3%)
 velvet-sim  denovo       Sim         6538167        2207    45      56810   2820.91   5348.36   6225757       123591(2%)

454 reads

 Type            #reads       min     max     mean
 454             77466        35      371     240


Pseudomonas aeruginosa b1 (PAb1)

References:

 Name           Length  %GC
 PA14           6537648 66.29
 PACS2          6492423 66.33
 PAO1           6264404 66.56
 ...

Solexa reads

 Type            #reads       min     max     mean
 Solexa          8627900      33      33      33    (~43X coverage)

Assemblies:

 Assembler      type         #ctgs   min     max     mean      stdev      ctgs-sum      #singletons    comments
 AMOSCmp-PA14   comparative  2053    17      170485  3011.84   11917.53   6183320       1127399
 AMOSCmp-PAO1   comparative  2797    17      75626   2161.19   5812.2     6044851       1592525
 AMOScmp-PA2192 comparative  5816    17      133129  1072.8    3725.22    6239454       1601299        largest assembly
 velvet         denovo       10684   45      16239   640.34    825.24     6841458       ?              much better than Ps !!!
 edena          denovo       11180   100     11300   552.36    610.52     6175460       3955865 (46%)  much better than Ps !!!
 sake           denovo       185030  34      5490    77.21   141.23  14287079

Merged assemblies(contigs&singletons):

 Assembler           type   input-data          #reads   #ctgs   min   max     mean    stdev      ctgs-sum       comments
 AMOSCmp-PA14-merge  ?      AMOSCmp-PA14(ctgs)  2053     1931    17    170485  3201.7  12981.57   6182486        2053-1931=122 gaps closed