akutils RADseq utility: Simplified processing of RADseq data through Stacks.

akutils: Andrews' Kang Utilities   

RADseq: Restriction Site Associated DNA Sequencing  

Largely inspired from my development of akutils for QIIME analyses, akutils RADseq utility functions similarly, using a custom parameters file to control various workflow options, but for RADseq data using Stacks for the main analysis component. This utility includes additional data preprocessing not offered in Stacks including combining of sample replicates and mapping out plastid genomes ahead of analysis. Upon analysis, you get all the usual Stacks output plus an additional output containing the files for processing your data in external packages such as Structure or Plink. When citing this workflow, you may cite this repository, but please make sure to also credit the hard work of real coders who developed the wonderful tools such as Stacks.