ddRADworkflows

Various workflows used for processing and analyzing ddRADSeq data.

ipyrad_workflows

ipyrad_workflow_shared.html

Contains workflows to process ddRADSeq data using the ipyrad toolkit. This was written for specific projects and datasets in the lab but could be useful for others. Includes all 7 assembly steps from demultiplexing and filtering to final assemblies, clustering threshold optimization, and branching to create assemblies for exploring different parameters of a dataset.

clustOpt.R

Code for running clustering optimization analyses and plotting results.

Relevant references:

• Eaton DAR & Overcast I. “ipyrad: Interactive assembly and analysis of RADseq datasets.” Bioinformatics (2020). https://doi.org/10.1093/bioinformatics/btz966
• McCartney-Melstad E, Gidiş M, Shaffer HB. An empirical pipeline for choosing the optimal clustering threshold in RADseq studies. Mol Ecol Resour. 2019; 19: 1195–1204. https://doi.org/10.1111/1755-0998.13029