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NGSEP specifications

Information


Unique identifier OMICS_00067
Name NGSEP
Alternative name Next Generation Sequencing Eclipse Plugin
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

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Publications for Next Generation Sequencing Eclipse Plugin

NGSEP citations

 (9)
library_books

Identification of Novel Alleles Conferring Superior Production of Rose Flavor Phenylethyl Acetate Using Polygenic Analysis in Yeast

2017
MBio
PMCID: 5676035
PMID: 29114020
DOI: 10.1128/mBio.01173-17

[…] parent strains with the s288c reference genome sequence but absent in the parent strains themselves (i.e., the same nucleotide was present in the two parent strains) were filtered out using the next-generation sequencing eclipse plugin (ngsep) program. the snp variant frequency was used for qtl mapping using the ngsep program in order to identify the genomic loci linked to high 2-peac […]

library_books

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis

2017
Comput Struct Biotechnol J
PMCID: 5295625
PMID: 28179981
DOI: 10.1016/j.csbj.2017.01.002

[…] tools, bowtie2 and the burrows-wheeler aligner (bwa) with 7 variant discovery programs: freebayes , the genome analysis toolkit (gatk) , the next generation sequencing experience platform (ngsep) , samtools , snver , varscan and vipr . from these tools, snver and vipr were particularly designed to identify variation in pools. because freebayes and gatk presented problems […]

library_books

The sole introduction of two single point mutations establishes glycerol utilization in Saccharomyces cerevisiae CEN.PK derivatives

2017
Biotechnol Biofuels
PMCID: 5209837
PMID: 28053667
DOI: 10.1186/s13068-016-0696-6

[…] and 85, respectively. whole-genome resequencing data can be accessed at the sra [], accession number srp093879., bioinformatic analysis of whole-genome resequencing data was performed following the ngsep pipeline v2.1.5 [] with the default parameters set on its graphical interface, except for the ploidy which was set to 1 and the minimum genotype quality score set to 60. in brief, the genotype […]

library_books

Combining Image Analysis, Genome Wide Association Studies and Different Field Trials to Reveal Stable Genetic Regions Related to Panicle Architecture and the Number of Spikelets per Panicle in Rice

2016
Front Plant Sci
PMCID: 5029283
PMID: 27703460
DOI: 10.3389/fpls.2016.01384

[…] et al., ) at cornell university. raw reads were demultiplexed and aligned to the rice reference genome (os-nipponbare-reference-irgsp-1.0) (kawahara et al., ), and variants were identified using the ngsep pipeline (duitama et al., ). this procedure provided a raw catalog of 690 thousand variable sites across the genome., from these panel, the following filters were applied to build a curated snp […]

library_books

Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP

2016
BMC Genomics
PMCID: 5009557
PMID: 27585926
DOI: 10.1186/s12864-016-2827-7

[…] 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 […]

library_books

Genomic saturation mutagenesis and polygenic analysis identify novel yeast genes affecting ethyl acetate production, a non selectable polygenic trait

2016
PMCID: 5349090
PMID: 28357348
DOI: 10.15698/mic2016.04.491

[…] sequence analysis using illumina hiseq2000 technology (bgi, hong kong, china). the sequence reads were mapped to the s288c reference sequence and variants were identified and filtered using the ngsep pipeline . tda1(4) and tda3(4) had accumulated respectively 815 and 967 single nucleotide polymorphisms (snps) and small indels compared to the original s288c strain. the genomic loci […]


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NGSEP institution(s)
Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Gerencia de Procesos, Centro Médico Imbanaco, Cali, Colombia
NGSEP funding source(s)
Supported by funding to CIAT provided by the Legumes, the Root Tubers and Bananas (RTB) and the Global Rice Science Partnership (GRiSP) programs of the CGIAR consortium, as well as the tropical legumes II project under the generation challenge program (GCP).

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