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Citations per year

Number of citations per year for the bioinformatics software tool NGSEP
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Tool usage distribution map

This map represents all the scientific publications referring to NGSEP per scientific context
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Protocols

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

 (11)
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

[…] ided to the Beijing Genomics Institute (BGI) (Hong Kong, China) for whole-genome sequence analysis, which was performed with the Illumina platform (HiSeq2000).Assembly and mapping were performed with NGSEP (next-generation sequencing eclipse plugin) (). Significance tests used to determine quantitative trait loci (QTLs) were conducted by the method of Claesen et al. (). […]

library_books

Testing Domestication Scenarios of Lima Bean (Phaseolus lunatus L.) in Mesoamerica: Insights from Genome Wide Genetic Markers

2017
Front Plant Sci
PMCID: 5601060
PMID: 28955351
DOI: 10.3389/fpls.2017.01551

[…] ón Sánchez (). These DNA samples were analyzed by GBS (Elshire et al., ) by the Institute for Genome Diversity of Cornell University, USA. Sequence reads were processed and analyzed with the software NGSEP (Duitama et al., ; Perea et al., ). Sequence reads were de-multiplexed on the basis of their unique barcodes and aligned to the common bean (Phaseolus vulgaris L.) genome used as reference. The […]

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

[…] The NGSEP-3.0.1 pipeline was used to discover SNPs and indels. This pipeline was executed with default parameters, except for the maximum number of alignments allowed to start at the same reference site, […]

call_split

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
call_split See protocol

[…] 95, 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 q […]

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 da […]

call_split

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

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

[…] The NGSEP Wizard is a new functionality which, starting from raw sequencing data, embodies all steps required to obtain a population variants file with only one execution screen. This functionality greatl […]


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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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