Software

pyRAD

Software to assemble de novo RADseq loci from restriction-site associated sequence data (RAD,ddRAD,GBS,PEddRAD,PEGBS). Alignment clustering allows for indel variation to better align highly divergent samples, merge and trim methods canbe employed to rescue overlapping paired end data, and reverse complement clustering is available to improve GBS assemblies of short overlapping contigs.

simrrls

Software to simulate fastQ formatted RAD, ddRAD or GBS data on an input species tree under a coalescent model. See example usage at this post.