GitHub:https://github.com/toczydlowski/stacks-on-htcondor

We ran the program Stacks (http://catchenlab.life.illinois.edu/stacks/; J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.) to assemble genetic data generated by genotyping by sequencing. We tested many Stacks assembly parameters in parallel on a high-throughput computing network (HTCondor). Our scripts for running this pipeline are housed on github at: https://github.com/toczydlowski/stacks-on-htcondor. These scripts will be made publicly available soon. We plan to publish a short note officially releasing and describing how to use these scripts.