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

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Title An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments
 
Creator Duitama, Jorge
Quintero, Juan Camilo
Cruz, Daniel Felipe
Quintero, Constanza
Hubmann, Georg
Foulquié Moreno, Maria R.
Verstrepen, Kevin J.
Trevelein, Johan M
Tohme, Joseph M.
 
Subject rice
arroz
genotypes
genotipos
 
Description 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.
 
Date 2014-01-11
2014-08-06T06:55:02Z
2014-08-06T06:55:02Z
 
Type Journal Article
 
Identifier Duitama J, Quintero JC, Cruz DF, Quintero C, Hubmann G, Foulquié-Moreno MR, Verstrepen KJ, Thevelein JM, and Tohme J. 2014. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Research. 42 (6): e44
0305-1048
https://hdl.handle.net/10568/41897
https://doi.org/10.1093/nar/gkt1381
 
Language en
 
Rights Open Access
 
Source Nucleic Acids Research