Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data.

Being able to assign sex to individuals and identify autosomal and sex‐linked scaffolds are essential in most population genomic analyses. Non‐model organisms often have genome assemblies at scaffold‐level and lack characterization of sex‐linked scaffolds. Previous methods to identify sex and sex‐linked scaffolds have relied on synteny between the non‐model organism and a closely related species or prior knowledge about the sex of the samples to identify sex‐linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here, we present "sex assignment through coverage" (SATC), a method to assign sex to samples and identify sex‐linked scaffolds from next generation sequencing (NGS) data. The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold‐level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: (i) male and female individuals, and (ii) sex‐linked scaffolds. This is achieved through projecting the scaffold depths into a low‐dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is freely available at https://github.com/popgenDK/SATC as R code and a graphical user interface (GUI). see also the Perspective by Iulia Darolti and Judith E. Mank. [ABSTRACT FROM AUTHOR]