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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 in publications

 (9)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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