Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.

BackgroundTherecent 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.ResultsHere 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.ConclusionsNGSEP 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2827-7) contains supplementary material, which is available to authorized users.

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El implante de stent en el conducto arterioso es una alternativa paliativa para neonatos con flujo pulmonar dependiente.Objetivo: Presentar una alternativa de acceso arterial para intervención percutánea en neonatos.Caso Clínico: Neonato a término con bajo peso, con diagnóstico de atresia pulmonar con septum interventricular intacto e hipoplasia grave de la válvula tricúspide con circulación coronaria dependiente. Por el riesgo quirúrgico y de daño arterial femoral y por la anatomía del conducto se decidió punción arterial axilar izquierda por donde se implantó exitosamente stent ductal coronario de 3,5 milímetros. Se presentó espasmo axilar que resolvió espontáneamente.Conclusión: Los accesos arteriales alternativos diferentes a la vía arterial femoral son una opción para neonatos de alto riesgo quirúrgico y bajo peso.