I have a pair ended HiSeq dataset obtained from a sort of RADseq experiment which i want to use to do a denovo assembly with. Now i have trimmed the reads using TrimGalore, but this left me with a bunch of reads of size 20 (the default minimum read length in TrimGalore).
I don't know if the reads are too short to actually use downstream. These small reads lower the optimal kmer estimations and will probably reduce quality of the assembly. I was wondering if there is some sort of method to decide the optimal minimum read length.
Thanks in advance,
With kind regards,