Assembly merge
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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