velvet assembly problem with parameters
Hi there I'm 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
• 2,729 views
•
link
updated
by
Ram
•
written
by
ilario.ferrocino •
•
written
by
ilario.ferrocino •
1 answer
Although I think it would be nice if you specify what you want to improve, 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 something interesting:
Log in to answer this question.
How did you conclude these results are bad? How do you think better results should look like? These inputs will help set some context.