ArticleNucleic acids research2013
QualitySNPng: a user-friendly SNP detection and visualization tool.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Resolving a century-old enigma: potato 'Bolters' originate from instability of the StCDF1.3 allele.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
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- Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Fine mapping of a thrips resistance QTL in Capsicum and the role of diterpene glycosides in the underlying mechanism.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Help or hindrance? The evolutionary impact of whole-genome duplication on immunogenetic diversity and parasite load.Ecology and evolution · 2020Article
- Genotyping of Multiple Clinical Samples with a Combined Direct PCR and Magnetic Lateral Flow Assay.iScience · 2018Article
- Article
- Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.BMC genomics · 2017Article
- Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta.PLoS genetics · 2017Article
- Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum.Genome biology and evolution · 2017Article
- SNP-markers in Allium species to facilitate introgression breeding in onion.BMC plant biology · 2016Article
- 4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information.BMC bioinformatics · 2016Article
- Transcriptome Analysis of Gerbera hybrida Including in silico Confirmation of Defense Genes Found.Frontiers in plant science · 2016Article
- NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.Nucleic acids research · 2015Article
- Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- High quality SNPs/Indels mining and characterization in ginger from ESTs data base.Bioinformation · 2015Article
- 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.).Frontiers in plant science · 2015Article
- Tomato breeding in the genomics era: insights from a SNP array.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
QualitySNPng is a new software tool for the detection and interactive visualization of single-nucleotide polymorphisms (SNPs). It uses a haplotype-based strategy to identify reliable SNPs; it is optimized for the analysis of current RNA-seq data; but it can also be used on genomic DNA sequences derived from next-generation sequencing experiments. QualitySNPng does not require a sequenced reference genome and delivers reliable SNPs for di- as well as polyploid species. The tool features a user-friendly interface, multiple filtering options to handle typical sequencing errors, support for SAM and ACE files and interactive visualization. QualitySNPng produces high-quality SNP information that can be used directly in genotyping by sequencing approaches for application in QTL and genome-wide association mapping as well as to populate SNP arrays. The software can be used as a stand-alone application with a graphical user interface or as part of a pipeline system like Galaxy. Versions for Windows, Mac OS X and Linux, as well as the source code, are available from http://www.bioinformatics.nl/QualitySNPng.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.