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QualitySNPng specifications


Unique identifier OMICS_00070
Name QualitySNPng
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes


No version available


  • person_outline Harm Nijveen
  • person_outline QSNPNG Team

Publication for QualitySNPng

QualitySNPng citations


Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum

Genome Biol Evol
PMCID: 5381655
PMID: 28082603
DOI: 10.1093/gbe/evw293

[…] R coding sequences using Bowtie 2 software with default parameters in sensitive mode (). The resulting ∼8200 and ∼7000 mapped reads of S. officinarum and S. spontaneum, respectively, were analyzed by QualitySNPng () aiming to identify specific SNPs of S. officinarum and S. spontaneum that are present in R570 haplotypes of LFY, PHYC, and TOR genes, including exons and introns.Indels (insertions/del […]


SNP markers in Allium species to facilitate introgression breeding in onion

BMC Plant Biol
PMCID: 5006257
PMID: 27576474
DOI: 10.1186/s12870-016-0879-0

[…] . After assembly, the average contig length varied from 309 bp for ‘Bravo’ to 649 for Pukekohe Longkeeper (Table ). The number of contigs ranged from 10,361 to 103,178. Analysis of these contigs with QualitySNPng showed that about 36 % contained reliable SNPs. For the RF genotype 7990 contigs containing a reliable SNP were identified and for the cultivars this number varied from 6709 to 38,520.For […]


High quality SNPs/Indels mining and characterization in ginger from ESTs data base

PMCID: 4369683
PMID: 25848168
DOI: 10.6026/97320630011085

[…] uation strategies for getting quality SNPs. There are many programs and pipelines for detection of SNPs viz; SEAN [] PolyPhred [] PolyBayes [] TRACE_DIFF [], HarvEST [], AutoSNP [], QualitySNP [] QualitySNPng []. QualitySNP has three filtering system to eliminate unreliable variations and to handle typical sequencing errors in absence of sequenced reference genome. Extracted SNPs information […]


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QualitySNPng institution(s)
Department of Plant Sciences, Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands; Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands; Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands; Department of Plant Sciences, Plant Breeding, Wageningen, The Netherlands
QualitySNPng funding source(s)
Supported by The Netherlands Consortium for Systems Biology, which is part of the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research.

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