Standard pipeline for denovo assembly

Question

[Bioblazer]

Hi all,

Is there any standard pipeline available for denovo assembly for with all genome size? example : I have 2 genome with varying genomic length one is about 5Kb(Phage phix) and another with 37Mb(Eukaryotic fungi). I want to know is there any pipeline so I can with that pipeline will I get precise result for both genome.

What is optimal kmer or atleast range of kmer values(for ex : 21 -31 ) to work with 5kb genome? Is it ok for 5kb genome can I go for 63mer or above?

[Medhat]

This is some suggestion but I do not know if there is something standard

RAMPART

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443680/figure/btv056-F1/

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation