ddRAD analysis pipeline

[Mattk]

Hi,

We are starting to generate ddRAD sequence data (as described by Peterson et al., 2012, http://www.plosone.org/article/info%...l.pone.0037135) for a variety of species which either have no reference genome, or have a genome that is under development. We would like to use the bioinformatic strategy these authors describe but cannot find a detailed description of the pipeline and I am unsure of how to connect the various scripts they have developed (https://github.com/brantp/rtd).

Does anyone have practical experience following their protocol?

Thanks in advance

[JackieBadger]

the ddRAD pipeline is a major hassle and generates huge temp files that are very impractical. We scrapped it and used STACKS which now incorporates ddRAD and is very easy to use