gihandjay / sfl_popgen

Research compendium for "Disentangling spatial, environmental, and demographic signals in population genomics of an exploited, estuarine-dependent flatfish."

Research compendium for "Disentangling spatial, environmental, and demographic signals in population genomics of an exploited, estuarine-dependent flatfish."

Raw reads underlying analysis available from short read archive (SRA): BioProject PRJNA754841.

Extended methods and results can be found in:

• Genotyping.Rmd: Contains details for read mapping, SNP calling, VCF filtering, and haplotyping of genomic data set used for analysis; the final genotyped file data/POPGEN/SFL.tidy.genotypes is too large to be uploaded to github, it is in a zipped folder (data/POPGEN/SFL.tidy).
• Analysis_SFL_PopGen.Rmd: Contains fully reproducible analysis (code + supplementary figures and tables) described as described in the paper

knitted html files for both analysis are included for easier viewing.

All necessary custom scripts & functions can be found in /scr.