kSNP

Finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation. kSNP3 now available.

Topic

Biology, Genetics, Molecular genetics, Genetic variation, DNA polymorphism

Detail

  • Operation: SNP detection

  • Software interface: Command-line interface

  • Language: Perl

  • License: -

  • Cost: Free

  • Version name: 3.1

  • Credit: Gardner SN, Hall BG.

  • Input: -

  • Output: -

  • Contact: barryghall at gmail.com, gardner26 at llnl.gov

  • Collection: -

  • Maturity: -

Publications

  • kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.
  • Gardner SN, et al. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. 2015; 31:2877-8. doi: 10.1093/bioinformatics/btv271
  • https://doi.org/10.1093/bioinformatics/btv271
  • PMID: 25913206
  • PMC: -
  • When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.
  • Gardner SN and Hall BG. When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. 2013; 8:e81760. doi: 10.1371/journal.pone.0081760
  • https://doi.org/10.1371/journal.pone.0081760
  • PMID: 24349125
  • PMC: PMC3857212

Download and documentation

< Back to DB search