Code: Genetic basis of sex determination in a parasitoid wasp species

This pipeline is part of the publication: Matthey-Doret et al., 2019, Genome Biology and evolution, doi: 10.1093/gbe/evz219
In this project, we use restriction-site associated DNA-sequencing (RAD-seq) and build a custom pipeline with the aim to locate and identify the complementary sex determination (CSD) locus/loci in the parasitoid wasp species Lysiphlebus fabarum. This repository contains a pipeline to map the reads using BWA and build loci using the different components of STACKS with optimal parameters and perform downstream analyses. It was designed to run on a distributed High Performance Computing (HPC) environment with LSF but can also be ran on a personal machine.