title: QualitySNPng: a user-friendly SNP detection and visualization tool.
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.
authors: Department of Plant Sciences, Laboratory of Bioinformatics, Wageningen University, PO Box 569, 6700AN Wageningen, The Netherlands. harm.nijveen@wur.nl
authors: Harm
authors: H
authors: Nijveen
authors: Martijn
authors: M
authors: van Kaauwen
authors: Danny G
authors: DG
authors: Esselink
authors: Brechtje
authors: B
authors: Hoegen
authors: Ben
authors: B
authors: Vosman
mesh_terms: D003196:Computer Graphics; D006239:Haplotypes; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D012984:Software
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