Jan 15, 2014

An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments

Nucleic Acids Research
Jorge DuitamaJoe Tohme

Abstract

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 separat...Continue Reading

Mentioned in this Paper

Rice (Dietary)
DNA Copy Number Changes
Genome
Computer Programs and Programming
Sorting - Cell Movement
Genomics
Sequencing
Massively-Parallel Sequencing
Nucleotides
High-Throughput Nucleotide Sequencing

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