Fig. 1From: From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife speciesOverview of methods used in this study to process reduced representation sequencing data with reference genomes, with some alternatives to software used indicated where appropriate. * Reproducibility filtering only possible if replicates or technical replicates are performed. ** Possible sex-linked SNP filter requires knowledge of sex of samples and is based on XX/XY system, but could be reversed for ZZ/ZW systemsBack to article page