Bioinformatic Analysis of Genotype By Sequencing (GBS) Data with NGSEP

The recent development and availability of different genotype by sequencing (GBS) protocols provided a cost-effective platform to perform high-resolution genomic analysis of entire populations in different species. The central component of all these protocols is the digestion of the initial DNA with known restriction enzymes, obtaining sequencing fragments in predictable sites. This allows to genotype thousands of genetic markers on populations with hundreds of individuals. Because GBS protocols achieve parallel genotyping through high throughput sequencing (HTS), every GBS protocol must include a bioinformatics pipeline for analysis of HTS data. Our bioinformatics group recently developed the Next Generation Sequencing Eclipse Plugin (NGSEP) for accurate, efficient, and user-friendly analysis of HTS data. Here we present the latest functionalities implemented in NGSEP in the context of the analysis of GBS data. Following parallel processing, merging and functional annotation of genotype calls from different samples, we added different filters for variants, samples and genotype calls as well as calculation of summary statistics overall and per sample, and diversity statistics per site. NGSEP includes a module to translate genotype calls to some of the most widely used input formats for integration with several tools to perform downstream analyses such as understanding the population structure, construction of genetic maps, and discovery of genes related to traits either by classical QTL analysis or by genome-wide association studies (GWAS). Results with different populations of cassava, beans, rice, and potato show that NGSEP is a powerful tool to facilitate the use of GBS protocols for population genomics.