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Ksnp website  

Description: identifies the pan-genome SNPs

Environment Modules

Run module spider Ksnp to find out what environment modules are available for this application.

System Variables

  • HPC_KSNP_DIR - installation directory
  • HPC_KSNP_BIN - executable directory
  • HPC_KSNP_DOC - documentation directory


If you publish research that uses Ksnp you have to cite it as follows:

Gardner, S.N., T. Slezak, and B.G. Hall. 2015. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genomes. Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271.

Gardner, S.N. and Hall, B.G. 2013. When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760

Gardner, S.N. and Slezak, T.R. 2010. Scalable SNP analyses of 100+ bacterial or viral genomes. Journal of Forensic Research, 1:107.