SNP4OrphanSpecies: A bio-informatic pipeline to isolate robust molecular markers for phylogeny, phylogeographical and population genetic studies in non-model species.

This pipeline performs a de-novo genome assembly, identifies single copy genes in the genome, and designs several pools of pair of primers for amplifying regions of these genes in multiplex. The pipeline is implemented in a SnakeMake workflow and uses Illumina data for the de-novo genome assembly. It was tested for Diplodia sapinea, a fungal pathogen causing severe infections in numerous conifers.