Commands and input files for population genetic analysis of Pacific Albacore using ddRADseq
Lists input commands used for STACKS and BWA, and subsequent filtering in VCFtools, plink, and paralog-finder (HDplot).
Maps used to select individuals and populations in STACKS runs.
Lists used to exclude certain loci in STACKS runs.
Ped and map files used by plink to estimate loci in LD.
Maps used to select subsets of individuals for estimating HWP.
R files for running loci filtering and population genetic analyses (e.g. whoa, adegenet, fsthet). I recommmend viewing original source GitHub pages and tutorials noted in each R file credits.
Sampling and sequence spreadsheets, genetic data (vcf, genepop, and structure genotype files, and the fasta consensus file for the 84 putatively adaptive loci), and full results for genome scan program and Fst analyses are available from Dryad: https://doi.org/10.5061/dryad.6djh9w103
Demultiplexed forward and reverse DNA sequence reads for the albacore sequenced in this study are openly available on the NCBI sequence read archive (SRA) under: PRJNA579774, http://www.ncbi.nlm.nih.gov/bioproject/579774
Available on request from Kathleen O'Malley (State Fisheries Genomics Lab, Oregon State University), https://agsci.oregonstate.edu/state-fisheries-lab/people
See this page: https://sites.google.com/view/evauxlution/data