Hello,

I have some RadSeq sequences from illumina sequencing. I have got my traditional R1 and R2 and I try to find out all fragment I might use for clustering. I used FLASH in order to assemble the fragments with matching ends:

.|<---------

.        ---------->|

I'm not interested in outies for now:

.     |<----------

---------->|

What I miss is the full elements:

|<-------->|

Knowing the primers at both ends, is there a way to extract all the fragments that are fully sequenced from both sides?

Thanks in advance,

Benjamin