title: Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP.
abstract: Therecent development and availability of different genotype by sequencing (GBS) protocols provided a cost-effective approach 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, to generate sequencing fragments at predictable and reproducible 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. We implemented a one step wizard to perform parallel read alignment, variants identification and genotyping from HTS reads sequenced from entire populations. 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 population structure analysis, construction of genetic maps, genetic mapping of complex traits and phenotype prediction for genomic selection. We assessed the accuracy of NGSEP on two highly heterozygous F1 cassava populations and on an inbred common bean population, and we showed that NGSEP provides similar or better accuracy compared to other widely used software packages for variants detection such as GATK, Samtools and Tassel.
  
  
  
  NGSEP is a powerful, accurate and efficient bioinformatics software tool for analysis of HTS data, and also one of the best bioinformatic packages to facilitate the analysis and to maximize the genomic variability information that can be obtained from GBS experiments for population genomics.
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.
authors: Claudia
authors: C
authors: Perea
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.
authors: Juan Fernando
authors: JF
authors: De La Hoz
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.
authors: Daniel Felipe
authors: DF
authors: Cruz
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.
authors: Juan David
authors: JD
authors: Lobaton
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.
authors: Paulo
authors: P
authors: Izquierdo
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.|Gerencia de Procesos, Centro Médico Imbanaco, Cali, 760033, Colombia.
authors: Juan Camilo
authors: JC
authors: Quintero
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia.
authors: Bodo
authors: B
authors: Raatz
authors: Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 763537, Colombia. j.duitama@cgiar.org.
authors: Jorge
authors: J
authors: Duitama
mesh_terms: D019295:Computational Biology; D017343:Genes, Plant; D005838:Genotype; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D002365:Manihot / Q000235:genetics; D027805:Phaseolus / Q000235:genetics; D017422:Sequence Analysis, DNA
keywords: Bioinformatics; GBS; NGSEP; SNP calling; Sequencing