QualitySNPng: a user-friendly SNP detection and visualization tool

H. Nijveen, M.P.W. van Kaauwen, G. Esselink, B. Hoegen, B. Vosman

Research output: Contribution to journalArticleAcademicpeer-review

23 Citations (Scopus)


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
Original languageEnglish
Pages (from-to)W587-W590
JournalNucleic acids research
Publication statusPublished - 2013


  • expressed sequence tags
  • generation
  • genome
  • discovery
  • alignment


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