RadSeq and short read

Question

[gbl1]

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

[jean.elbers]

What is the objective of the RADseq project you are working on? Might I suggest STACKS (http://catchenlab.life.illinois.edu/stacks/) or ipyrad (https://ipyrad.readthedocs.io/) or dDocent (http://www.ddocent.com/) for the analysis?

[gbl1]

I try to compare several individuals on presence/absence of all sequences.

I'll have a look at your programs

Thanks