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QQ-SNV

QQ-SNV

A tool to detect single nucleotide polymorphism (SNP) in heterogeneous virus population from Illumina sequencing data. The QQ-SNV algorithm uses a logistic regression classifier model based on quantiles of quality scores.

Topic

Genetic variation

Details

  • Operation: SNP detection
  • Input: FASTA,SAM
  • Output: -
  • Software interface: Command-line user interface
  • Language: Perl;SAS 9.2
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL
  • Cost: Free
  • Version name: -
  • Credit: -
  • Contact: jaerssen _at_ its.jnj.com | kvdborgh _at_ its.jnj.com
  • Collection: -

Publications

Van der Borght K, Thys K, Wetzels Y, Clement L, Verbist B, Reumers J, van Vlijmen H, Aerssens J "QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles." BMC Bioinformatics. 2015 Nov 10;16:379. https://doi.org/10.1186/s12859-015-0812-9
PMID: 26554718
PMCID: PMC4641353


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