I am planning to use Kmergenie for Kmer estimation for de novo assembly of eukaryotic genome of size 1Gb. I have Paired end library and mate pair library of three different insert sizes. I wanted to know, if I should use paired end and MP library as input together or should I carry out Kmer estimation separately for each library.
I intent using AbySS or SOAPdenovo2 for assembly.
Thanks for you help.