NYC-oyster-admixture

This repository stores scripts for Hudson River Raritan and Long Island Sound oyster admixture manuscript "Spatial and temporal admixture patterns from farm oysters supplementing wild population recruitment" (https://doi.org/10.1111/mec.70354). An archive of this repo has been deposited on Dryad https://doi.org/10.5061/dryad.08kprr5hv.

• ddRAD: scripts processing & analyzing ddRAD-Seq data
• lcWGS: scripts processing & analyzing low coverage WGS data
• figures: collection of scripts generating figures
• nemo_simulation: scripts performing nemo simulations and analyzing simulation results
• misc: comparison between ddRAD and lcWGS, coding region test, etc.

Acknowledgements

Scripts processing lcWGS data are mostly modified from Therkildsen Lab scripts for low coverage whole-genome sequencing data processing and analysis.

• Tutorials for analysis of low-coverage whole genome sequencing data
• dDocent RADSeq Bioinformatics
• Dr. Honggang Zhao's code repo
• Nemo Simulator