Panoramic: A package for constructing eukaryotic pan-genomes.

The study of intraspecific genomic variation in eukaryotic species has been the focus of numerous genome resequencing projects in recent years. One emerging approach for the analysis of intraspecific diversity uses the concept of a pan-genome, which theoretically represents the full set of genomic sequences and coding genes from all individuals of a given species. This approach has many advantages over reference-based methods and has been successfully applied to study both prokaryotic and eukaryotic species. However, the process of pan-genome construction still presents considerable scientific and technical challenges, especially for eukaryotic species with large and complex genomes. Although general approaches for the construction of pan-genomes have been devised, currently available software tools implement only certain modules of the entire computational procedure. Therefore, each pan-genome project requires the development of tailored analysis pipelines, thus complicating and prolonging the process and impairing research reproducibility and comparison across studies. Here, we present Panoramic, a software package for the automatic construction of eukaryotic pan-genomes. Panoramic takes raw sequencing reads as input and applies two alternative approaches for pan-genome construction. Panoramic makes pan-genome construction a considerably easier task by providing simple user interface and efficient data processing algorithms. We demonstrate the use of Panoramic by constructing the pan-genome of the model plant species Arabidopsis thaliana from sequencing data of 20 diverse ecotypes.