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Protocols

kSNP specifications

Information


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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Documentation


Maintainer


  • person_outline Barry G. Hall

Publications for kSNP

kSNP citations

 (77)
call_split

Genomic diversity of Taylorella equigenitalis introduced into the USA from 1978 to 2012

2018
PLoS One
PMCID: 5870977
PMID: 29584782
DOI: 10.1371/journal.pone.0194253
call_split See protocol

[…] olates were selected for the study, all 200 isolates of T. equigenitalis from the NVSL’s isolate repository were initially sequenced using an Illumina MiSeq, de novo assembled and then analyzed using kSNP (methods described below). Five diverse isolates were then selected for this study () which represented each major branch in this tree. Within clade selection of each isolate was guided using PFG […]

library_books

Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

2018
PMCID: 5845375
PMID: 29556252
DOI: 10.1186/s13099-018-0238-9

[…] o assemblies reported in this study, and those reported earlier by Chase et al. [] and the genome of C. sakazakii strain Cro2819A3 (Table ). As indicated in Fig. , the whole genome analysis using the kSNP3 algorithm showed a similar pattern of phylogenetic relatedness among the strains where the German PIF strains (Csak GK-series) clustered together (some indistinguishable among them) with the oth […]

library_books

Expansion of a urethritis associated Neisseria meningitidis clade in the USA with concurrent acquisition of N. gonorrhoeae alleles

2018
BMC Genomics
PMCID: 5834837
PMID: 29499642
DOI: 10.1186/s12864-018-4560-x

[…] 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. 13 […]

library_books

Whole Genome Sequencing characterization of bloodstream infection causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374

2018
PMCID: 5955473
PMID: 29338592
DOI: 10.1080/21505594.2017.1421894

[…] y 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 compa […]

library_books

Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug resistant SNPs using whole genome sequencing

2018
J Biomed Sci
PMCID: 5815235
PMID: 29448938
DOI: 10.1186/s12929-018-0414-8

[…] A parsimony tree with respect to reference and 10 isolates was generated from the kSNP3 pipeline, parsimony tree is consensus tree based on all of the SNPs identified between the reference genome TIGR4 and the 10 isolates. Branch lengths are expressed in terms of changes per number […]

library_books

Phenotypic and Genotypic Analysis of Antimicrobial Resistance among Listeria monocytogenes Isolated from Australian Food Production Chains

2018
Genes
PMCID: 5852576
PMID: 29425131
DOI: 10.3390/genes9020080

[…] 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 (https: […]

Citations

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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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