Pronghorn population genomics show connectivity at the core of their range

This directory contains data, protocols, and scripts associated with our publication. The data include sample metadata, microsatellite genotypes, SNP genotypes, SNP genotype likelihoods, and the consensus genome used for de novo assembly of our raw sequencing reads. The protocols include our genotyping-by-sequencing library preparation protocol. We include Unix-based scripts for our step-by-step bioinformatics workflow, for parsing raw sequence data by sample barcode, for data reduction before CD-HIT assembly, for running bwa in parallel, for converting vcf genotypes into a genotype likelihood matrix, and for converting a genotype likelihood matrix into a text file. We also include R-based scripts for performing PCA on SNP data, for performing our rare variant analysis, and for detecting loci with excess levels of heterozygosity.