Question: velvet assembly problem with parameters
0
gravatar for ilario.ferrocino
4.3 years ago by
European Union
ilario.ferrocino0 wrote:

Hi there im try to do assembly with velvet  on my metagenomic illumina single end sequence. 

I'had try to use different kmer value but i have bad results like this:

How i can fix it??

 

parameters -short sample name total number contigs total contig length largest contig length mean/median contig length N50 (bp)
assembly kmer 53 e ins 300 09.TO 189,412 146,667,097 54,723 774/493 914
assembly kmer 63 e ins 300 09.TO 178,173 132,535,391 85,044 744/470 832
assembly kmer 82 e ins 300 09.TO 146,108 103,053,100 177,456 705/436 746
assembly kmer 77 e ins 300 09.TO 155,024 110,414,760 151,465 712/442 756
assembly kmer 60 e ins 300 09.TO 182,064 138,638,656 63,991 761/478 873
assembly kmer 50 e ins 300 09.TO 194.84 152,368,820 51,381 782/501 932
velvet assembly • 1.4k views
ADD COMMENTlink modified 4.2 years ago by dago2.5k • written 4.3 years ago by ilario.ferrocino0
1

How did you conclude these results are bad? How do you think better results should look like? These inputs will help set some context.

ADD REPLYlink written 4.3 years ago by RamRS21k
0
gravatar for dago
4.2 years ago by
dago2.5k
Germany
dago2.5k wrote:

Although I think it would be nice if you specify what you want to inprove, I think you can take a look at this program:

VelvetOptimiser

Maybe you could also try different assembly strategy, in this paper there might be somethign interesting:

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Evaluation of short read metagenomic assembly

Sequence assembly demystified

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by dago2.5k
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