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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

PMCID: 5381655
PMID: 28082603
DOI: 10.1093/gbe/evw293

[…] 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 […]


SNP markers in Allium species to facilitate introgression breeding in onion

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

[…] into any contig, and; f) a minimum contig length of 180 bp is required. contigs were constructed for each genotype separately and for the onion genotypes combined., all contigs were submitted to qualitysnpng for snp discovery using the default settings of the programme [, ]. qualitysnpng is designed for filtering out snps from paralogous sequences without prior knowledge about the reference […]


Transcriptome Analysis of Gerbera hybrida Including in silico Confirmation of Defense Genes Found

PMCID: 4771743
PMID: 26973688
DOI: 10.3389/fpls.2016.00247

[…] transcriptome using bowtie2 (–very-sensitive setting) and filtered for mapping quality (>2) using samtools (li et al., ). the resulting sam files were merged and used for snp calling using qualitysnpng (nijveen et al., ) with default settings. retrieved snp regions were blasted (blastn, e-value: 1e-30) to the contigs derived from the est sequences as a control for possible paralog […]


Using RNA Seq to assemble a rose transcriptome with more than 13,000 full length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)

PMCID: 4404716
PMID: 25954285
DOI: 10.3389/fpls.2015.00249

[…] bowtie 2 (langmead and salzberg, ) with modified settings (—very-sensitive—rfg 5, 10) and filtered for map quality (>25) using samtools., the resulting sam file was used for snp calling using qualitysnpng (nijveen et al., ) with modified settings (the minimal similarity score per polymorphic site, similarityallpolymorphicsites: 0.8, the minimal number of reads per allele set at 5). using […]


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

PMCID: 4369683
PMID: 25848168
DOI: 10.6026/97320630011085

[…] 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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