The general workflow is to process an entire ddRADseq data set, from raw sequencing reads to creating input files for commonly used programs.
There are specific instructions in each subdirectory of this pipeline.
This pipeline was written for and tested on Stacks v1.35. If you are using a newer version, I can't guarantee this will be compatible.
Citation Information:
Using the pipeline. The scripts involved with this pipeline were originally published as part of the following work:
- Portik, D.M., Leache, A.D., Rivera, D., Blackburn, D.C., Rodel, M.-O., Barej, M.F., Hirschfeld, M., Burger, M., and M.K. Fujita. 2017. Evaluating mechanisms of diversification in a Guineo-Congolian forest frog using demographic model selection. Molecular Ecology, 26: 5245-5263. https://doi.org/10.1111/mec.14266
If you use or modify this script for your own purposes, please cite this publication.
Contact:
Daniel Portik, PhD
Postdoctoral Researcher
University of Arizona