Introduction

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.

Publications

  1. QualitySNPng: a user-friendly SNP detection and visualization tool.
    Cite this
    Nijveen H, van Kaauwen M, Esselink DG, Hoegen B, Vosman B, 2013-07-01 - Nucleic Acids Research

Credits

  1. Harm Nijveen
    Developer

  2. Martijn van Kaauwen
    Developer

  3. Danny G Esselink
    Developer

  4. Brechtje Hoegen
    Developer

  5. Ben Vosman
    Investigator

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Summary
AccessionBT001421
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByBen Vosman