kSNP protocols

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kSNP specifications


Unique identifier OMICS_08467
Name kSNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of the paths to the original genome files.
Operating system Unix/Linux, Mac OS
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 3.0.21
Stability Stable
Maintained Yes



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  • person_outline Barry G. Hall <>

Publications for kSNP

kSNP in pipelines

PMCID: 5955473
PMID: 29338592
DOI: 10.1080/21505594.2017.1421894

[…] table s3). the phylogeny scheme was generated from the 429,267 ksnp3-detected snp sites for all the chromosome sequences with k = 21, as determined by kchooser []. a parsimony tree was generated by ksnp3 based on an extended majority rule consensus of the equally most parsimonious trees from a sample of 100 trees []. the tree was displayed with itol with midpoint rooting []., genome sequence […]

PMCID: 5398294
PMID: 28379509
DOI: 10.1093/gbe/evx062

[…] performing a blastx search in the ncbi genbank nr database and using the predicted protein of the query sequences under the thresholds of the highest bit-score and e-value (≤ 1e-03)., we constructed ksnp trees, genome-wide trees, and pan-genome trees using whole-genome sequence data of 106 s. suis and other streptococcus spp. strains ( and , online). all of the trees demonstrated that s. suis […]

kSNP in publications

PMCID: 5870977
PMID: 29584782
DOI: 10.1371/journal.pone.0194253

[…] 15kb-20kb insert size (bluepippin kit) and sequenced on an rs ii (pacific biosciences, menlo park, ca) with 2 smrt cells per sample., short-read sequences were de novo assembled using abyss [] for ksnp analysis. pacbio reads were assembled using hgap version 2.0 with the default parameters []. canu version 1.4 was also used to assemble raw pacbio reads []. mauve was used to align the output […]

PMCID: 5834837
PMID: 29499642
DOI: 10.1186/s12864-018-4560-x

[…] gonorrhoeae sequence typing for antimicrobial resistance (ng-star) [] analyses for further characterization., snp-based parsimony phylogenies (fig. ) were inferred from genome assemblies by the ksnp v3.0 pipeline []. ksnp examines all 25 bp sequences in each genome (k-mers) and reports core single nucleotide polymorphisms (snps) for all sets of k-mers that differ only at the central (i.e. […]

PMCID: 5955473
PMID: 29338592
DOI: 10.1080/21505594.2017.1421894

[…] regularly interspaced short palindromic repeats) arrays were identified by pilercr []., genome-wide single nucleotide polymorphism (snp) calling and phylogenetic analysis was performed by using ksnp v3 []. the 106 completely sequenced k. pneumoniae genomes, including rjf293 sequenced in this study, were downloaded from ncbi genome (supplementary table s3). the phylogeny scheme was generated […]

PMCID: 5815235
PMID: 29448938
DOI: 10.1186/s12929-018-0414-8

[…] of minimum edge weight set to 5 and the minimum edge density (total number of edges / theoretical number of edges) set to 0.35., single nucleotide polymorphisms (snps) were identified using ksnp3 program (version 3.021) which identifies pan-genome snps in a set of genome sequences and builds a phylogenetic tree based on the snps []. ksnp3 was run using the standard mode of snp detection […]

PMCID: 5852576
PMID: 29425131
DOI: 10.3390/genes9020080

[…] in australia, such as st1, st2, st3, st155, and st204 []. a list of amr genes used in blast searches is presented in ., the single-nucleotide polymorphism (snp) phylogeny was determined with ksnp v3.1 [] for 79 isolates using a mixture of finished genomes, draft genomes, and read data. paired-end read files were quality filtered, converted to fasta and merged using seqtk v1.2–r102 […]

kSNP institution(s)
Computations/Global Security, Lawrence Livermore National Laboratory, Livermore, CA, USA; Bellingham Research Institute, Bellingham, WA, USA
kSNP funding source(s)
Supported under internal funding at LLNL.

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