Is there a program dealing with degenerate base region (DBRs) (ddRAD seq protocol)?

[beausoleilmo]

I use ddRADseq with DBR to deal with PCR duplicates. We basically add a DBR, in the Read2 paired end.

My questions are:

1. How can we deal with DBR bioinformatically? Is there a software that can deal with the DBRs?
2. It seems that Stacks has different options to do this. If you go on their manual it seems that their Oligo sequence options for the clone_filter could do the trick. But it's unclear on how to apply it or if it's designed to deal with DBRs. Did someone used it before?

The references I base my protocol on are below:

Schweyen, H., Rozenberg, A., & Leese, F. (2014). Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters. The Biological Bulletin, 227(2), 146–160.

Tin, M. M. Y., Rheindt, F. E., Cros, E., & Mikheyev, A. S. (2014). Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy. Molecular Ecology Resources, 15(2), 329–336.

[cbird]

If Schweyen, H., Rozenberg, A., & Leese, F. (2014) didn't make a tool, then you'll probably have to use basic command line tools to make a script. Useful commands include grep or agrep, cdhit, uniq. There are other papers out there that employ some sort of degenerate base sequence to id rad frags and may help you identify a useful script that can be adapted: RADcap, quaddRad, etc

I'm wondering what your coefficient of variation (stdev/mean) for coverage per individual is for the Schweyen et al 2014 method? If you look at their results, there is notably elevated variance when they employ the DBR.