Use Skesa on 50bp read length sequence

[abcdtree]

I am trying to use Skesa on 50bp read length sequence instead of 150bp.
I found the result is not as good as the 150bp cases.
Do you have any recommendation on settings or parameters or pre-jobs to help to ensure the assembly quality?
(I have tried to set the kmer as [21,25,29,33,37])
Thanks,

Josh

[souvorov]

50bp reads are not very good for assembling. The default parameters are probably the way to go. There is no point in increasing kmer - SKESA iterates through larger kmers internally. If anything, you may try decrease kmer to 19 or even 17.